diff --git a/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml b/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml index b16fc44..2b46912 100644 --- a/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml +++ b/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + De novo multiple sequence alignment with MAFFT + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version alignment q2galaxy run alignment mafft '$inputs' diff --git a/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml b/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml index 7010372..5ee50dd 100644 --- a/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml +++ b/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Add sequences to multiple sequence alignment with MAFFT. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version alignment q2galaxy run alignment mafft_add '$inputs' @@ -36,6 +39,7 @@ for:
+
diff --git a/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml b/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml index 91816ce..9e7936f 100644 --- a/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml +++ b/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Positional conservation and gap filtering. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version alignment q2galaxy run alignment mask '$inputs' diff --git a/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml b/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml index 9f1c8b1..c507441 100644 --- a/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml +++ b/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Add pseudocount to table. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version composition q2galaxy run composition add_pseudocount '$inputs' diff --git a/tools/suite_qiime2__composition/qiime2__composition__ancom.xml b/tools/suite_qiime2__composition/qiime2__composition__ancom.xml index b0eff91..0a691d5 100644 --- a/tools/suite_qiime2__composition/qiime2__composition__ancom.xml +++ b/tools/suite_qiime2__composition/qiime2__composition__ancom.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Apply ANCOM to identify features that differ in abundance. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version composition q2galaxy run composition ancom '$inputs' diff --git a/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml b/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml index 2100ac0..29d06c4 100644 --- a/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml +++ b/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Analysis of Composition of Microbiomes with Bias Correction + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version composition q2galaxy run composition ancombc '$inputs' diff --git a/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml b/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml index bcf9e31..a06df53 100644 --- a/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml +++ b/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Differential abundance bar plots + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version composition q2galaxy run composition da_barplot '$inputs' diff --git a/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml b/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml index 85e05b5..6909c79 100644 --- a/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml +++ b/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + View tabular output from ANCOM-BC. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version composition q2galaxy run composition tabulate '$inputs' diff --git a/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza b/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza index b8feafc..caac80f 100644 Binary files a/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza and b/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza differ diff --git a/tools/suite_qiime2__composition/test-data/ancombc.test1.table.qza b/tools/suite_qiime2__composition/test-data/ancombc.test1.table.qza index b8feafc..caac80f 100644 Binary files a/tools/suite_qiime2__composition/test-data/ancombc.test1.table.qza and b/tools/suite_qiime2__composition/test-data/ancombc.test1.table.qza differ diff --git a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_paired.xml b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_paired.xml index ef1318d..44f41d8 100644 --- a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_paired.xml +++ b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_paired.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Demultiplex paired-end sequence data with barcodes in-sequence. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version cutadapt q2galaxy run cutadapt demux_paired '$inputs' diff --git a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml index e5397b1..da9e5b5 100644 --- a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml +++ b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Demultiplex single-end sequence data with barcodes in-sequence. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version cutadapt q2galaxy run cutadapt demux_single '$inputs' diff --git a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml index ec2f1ba..940463c 100644 --- a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml +++ b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Find and remove adapters in demultiplexed paired-end sequences. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version cutadapt q2galaxy run cutadapt trim_paired '$inputs' diff --git a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml index e858770..c7beae5 100644 --- a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml +++ b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Find and remove adapters in demultiplexed single-end sequences. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version cutadapt q2galaxy run cutadapt trim_single '$inputs' diff --git a/tools/suite_qiime2__cutadapt/test-data/demux_paired.test0.seqs.qza b/tools/suite_qiime2__cutadapt/test-data/demux_paired.test0.seqs.qza index 81f07d2..3645a80 100644 Binary files a/tools/suite_qiime2__cutadapt/test-data/demux_paired.test0.seqs.qza and b/tools/suite_qiime2__cutadapt/test-data/demux_paired.test0.seqs.qza differ diff --git a/tools/suite_qiime2__cutadapt/test-data/demux_single.test0.seqs.qza b/tools/suite_qiime2__cutadapt/test-data/demux_single.test0.seqs.qza index 97f8f1f..433a1fb 100644 Binary files a/tools/suite_qiime2__cutadapt/test-data/demux_single.test0.seqs.qza and b/tools/suite_qiime2__cutadapt/test-data/demux_single.test0.seqs.qza differ diff --git a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_ccs.xml b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_ccs.xml index 61bd86a..50f6e4b 100644 --- a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_ccs.xml +++ b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_ccs.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Denoise and dereplicate single-end Pacbio CCS + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version dada2 q2galaxy run dada2 denoise_ccs '$inputs' @@ -33,13 +36,23 @@ for: value is not None and len(value) > 0 - - - - - value is not None and len(value) > 0 -
+ + + + + + + + + + + + + + + + diff --git a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml index d430b85..189d18f 100644 --- a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml +++ b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Denoise and dereplicate paired-end sequences + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version dada2 q2galaxy run dada2 denoise_paired '$inputs' diff --git a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml index 0a72d90..505dec2 100644 --- a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml +++ b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Denoise and dereplicate single-end pyrosequences + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version dada2 q2galaxy run dada2 denoise_pyro '$inputs' diff --git a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml index a7786f5..0b312e8 100644 --- a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml +++ b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Denoise and dereplicate single-end sequences + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version dada2 q2galaxy run dada2 denoise_single '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]'] diff --git a/tools/suite_qiime2__dada2/test-data/denoise_paired.test0.demux-paired.qza b/tools/suite_qiime2__dada2/test-data/denoise_paired.test0.demux-paired.qza index 31fb45a..7cc7c2a 100644 Binary files a/tools/suite_qiime2__dada2/test-data/denoise_paired.test0.demux-paired.qza and b/tools/suite_qiime2__dada2/test-data/denoise_paired.test0.demux-paired.qza differ diff --git a/tools/suite_qiime2__dada2/test-data/denoise_single.test0.demux-single.qza b/tools/suite_qiime2__dada2/test-data/denoise_single.test0.demux-single.qza index 17293ef..d213ed8 100644 Binary files a/tools/suite_qiime2__dada2/test-data/denoise_single.test0.demux-single.qza and b/tools/suite_qiime2__dada2/test-data/denoise_single.test0.demux-single.qza differ diff --git a/tools/suite_qiime2__deblur/qiime2__deblur__denoise_16S.xml b/tools/suite_qiime2__deblur/qiime2__deblur__denoise_16S.xml index 95682c7..226ccfa 100644 --- a/tools/suite_qiime2__deblur/qiime2__deblur__denoise_16S.xml +++ b/tools/suite_qiime2__deblur/qiime2__deblur__denoise_16S.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Deblur sequences using a 16S positive filter. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version deblur q2galaxy run deblur denoise_16S '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]'] diff --git a/tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml b/tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml index bb05c30..2e3de4a 100644 --- a/tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml +++ b/tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Deblur sequences using a user-specified positive filter. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version deblur q2galaxy run deblur denoise_other '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]'] diff --git a/tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml b/tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml index 4f4532d..e0d1813 100644 --- a/tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml +++ b/tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Visualize Deblur stats per sample. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version deblur q2galaxy run deblur visualize_stats '$inputs' diff --git a/tools/suite_qiime2__deblur/test-data/denoise_16S.test0.demux-filtered.qza b/tools/suite_qiime2__deblur/test-data/denoise_16S.test0.demux-filtered.qza index 037ac0d..cc9ac34 100644 Binary files a/tools/suite_qiime2__deblur/test-data/denoise_16S.test0.demux-filtered.qza and b/tools/suite_qiime2__deblur/test-data/denoise_16S.test0.demux-filtered.qza differ diff --git a/tools/suite_qiime2__deblur/test-data/visualize_stats.test0.deblur-stats.qza b/tools/suite_qiime2__deblur/test-data/visualize_stats.test0.deblur-stats.qza index ca1cc92..29cdf67 100644 Binary files a/tools/suite_qiime2__deblur/test-data/visualize_stats.test0.deblur-stats.qza and b/tools/suite_qiime2__deblur/test-data/visualize_stats.test0.deblur-stats.qza differ diff --git a/tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml b/tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml index 426cfa0..f01b922 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Demultiplex paired-end sequence data generated with the EMP protocol. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version demux q2galaxy run demux emp_paired '$inputs' diff --git a/tools/suite_qiime2__demux/qiime2__demux__emp_single.xml b/tools/suite_qiime2__demux/qiime2__demux__emp_single.xml index 94dd33d..25caa36 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__emp_single.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__emp_single.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Demultiplex sequence data generated with the EMP protocol. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version demux q2galaxy run demux emp_single '$inputs' diff --git a/tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml b/tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml index eaf1e67..be92ed7 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter samples out of demultiplexed data. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version demux q2galaxy run demux filter_samples '$inputs' @@ -23,9 +26,9 @@ for: + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]'] diff --git a/tools/suite_qiime2__demux/qiime2__demux__partition_samples_paired.xml b/tools/suite_qiime2__demux/qiime2__demux__partition_samples_paired.xml index d44939b..ad103c4 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__partition_samples_paired.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__partition_samples_paired.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Split demultiplexed sequence data into partitions. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version demux q2galaxy run demux partition_samples_paired '$inputs' diff --git a/tools/suite_qiime2__demux/qiime2__demux__partition_samples_single.xml b/tools/suite_qiime2__demux/qiime2__demux__partition_samples_single.xml index 3691fa9..6b526e3 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__partition_samples_single.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__partition_samples_single.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Split demultiplexed sequence data into partitions. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version demux q2galaxy run demux partition_samples_single '$inputs' @@ -21,11 +24,12 @@ for: - + + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[SequencesWithQuality]'] + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[SequencesWithQuality]']
diff --git a/tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml b/tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml index 512a9e8..364f269 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Subsample paired-end sequences without replacement. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version demux q2galaxy run demux subsample_paired '$inputs' diff --git a/tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml b/tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml index f909954..fb9f6e8 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Subsample single-end sequences without replacement. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version demux q2galaxy run demux subsample_single '$inputs' diff --git a/tools/suite_qiime2__demux/qiime2__demux__summarize.xml b/tools/suite_qiime2__demux/qiime2__demux__summarize.xml index e2a69c9..0ae4dc0 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__summarize.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__summarize.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Summarize counts per sample. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version demux q2galaxy run demux summarize '$inputs' @@ -23,9 +26,9 @@ for: + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]'] diff --git a/tools/suite_qiime2__demux/qiime2__demux__tabulate_read_counts.xml b/tools/suite_qiime2__demux/qiime2__demux__tabulate_read_counts.xml index d4b88f1..0e3b275 100644 --- a/tools/suite_qiime2__demux/qiime2__demux__tabulate_read_counts.xml +++ b/tools/suite_qiime2__demux/qiime2__demux__tabulate_read_counts.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Tabulate counts per sample + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version demux q2galaxy run demux tabulate_read_counts '$inputs' @@ -23,9 +26,9 @@ for: + - diff --git a/tools/suite_qiime2__demux/test-data/emp_single.test0.sequences.qza b/tools/suite_qiime2__demux/test-data/emp_single.test0.sequences.qza index ac8c541..b07df8f 100644 Binary files a/tools/suite_qiime2__demux/test-data/emp_single.test0.sequences.qza and b/tools/suite_qiime2__demux/test-data/emp_single.test0.sequences.qza differ diff --git a/tools/suite_qiime2__demux/test-data/summarize.test0.demux.qza b/tools/suite_qiime2__demux/test-data/summarize.test0.demux.qza index 6014454..8d1ca13 100644 Binary files a/tools/suite_qiime2__demux/test-data/summarize.test0.demux.qza and b/tools/suite_qiime2__demux/test-data/summarize.test0.demux.qza differ diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml b/tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml index 65a6469..440d68c 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + adonis PERMANOVA test for beta group significance + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity adonis '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml index 810c3b2..f6ed81b 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Alpha diversity + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity alpha '$inputs' @@ -24,8 +27,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml index 0680929..189ddd8 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Alpha diversity correlation + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity alpha_correlation '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml index bbd7c2e..288f261 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Alpha diversity comparisons + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity alpha_group_significance '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml index 1d18f29..aa86a63 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Alpha diversity (phylogenetic) + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity alpha_phylogenetic '$inputs' @@ -24,8 +27,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml index b03e8bc..12106be 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Alpha rarefaction curves + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity alpha_rarefaction '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta.xml index 16afc14..b6526f8 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__beta.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta diversity + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity beta '$inputs' @@ -24,8 +27,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml index 3bfcedb..d325da7 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta diversity correlation + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity beta_correlation '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml index 0dd55ca..de9af34 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta diversity group significance + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity beta_group_significance '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml index 577823a..c5b54d3 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta diversity (phylogenetic) + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity beta_phylogenetic '$inputs' @@ -24,8 +27,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml index 068889e..9f32620 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta diversity rarefaction + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity beta_rarefaction '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml b/tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml index 9043e47..e1cdb93 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + bioenv + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity bioenv '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics.xml b/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics.xml index 3fc1e27..2aa6e02 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Core diversity metrics (non-phylogenetic) + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity core_metrics '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics_phylogenetic.xml b/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics_phylogenetic.xml index 8cfa229..afa16ce 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics_phylogenetic.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics_phylogenetic.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Core diversity metrics (phylogenetic and non-phylogenetic) + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity core_metrics_phylogenetic '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__filter_alpha_diversity.xml b/tools/suite_qiime2__diversity/qiime2__diversity__filter_alpha_diversity.xml index 3d6659c..a017513 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__filter_alpha_diversity.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__filter_alpha_diversity.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter samples from an alpha diversity metric. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity filter_alpha_diversity '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__filter_distance_matrix.xml b/tools/suite_qiime2__diversity/qiime2__diversity__filter_distance_matrix.xml index 43b61a8..1e63b93 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__filter_distance_matrix.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__filter_distance_matrix.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter samples from a distance matrix. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity filter_distance_matrix '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__mantel.xml b/tools/suite_qiime2__diversity/qiime2__diversity__mantel.xml index b94e89f..c77c3c8 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__mantel.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__mantel.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Apply the Mantel test to two distance matrices + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity mantel '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__partial_procrustes.xml b/tools/suite_qiime2__diversity/qiime2__diversity__partial_procrustes.xml index ff3289d..ebb01c3 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__partial_procrustes.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__partial_procrustes.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Partial Procrustes + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity partial_procrustes '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__pcoa.xml b/tools/suite_qiime2__diversity/qiime2__diversity__pcoa.xml index ba116af..1a95080 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__pcoa.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__pcoa.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Principal Coordinate Analysis + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity pcoa '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__pcoa_biplot.xml b/tools/suite_qiime2__diversity/qiime2__diversity__pcoa_biplot.xml index d5e4215..939d78e 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__pcoa_biplot.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__pcoa_biplot.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Principal Coordinate Analysis Biplot + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity pcoa_biplot '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__procrustes_analysis.xml b/tools/suite_qiime2__diversity/qiime2__diversity__procrustes_analysis.xml index d768576..dcb1602 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__procrustes_analysis.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__procrustes_analysis.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Procrustes Analysis + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity procrustes_analysis '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__tsne.xml b/tools/suite_qiime2__diversity/qiime2__diversity__tsne.xml index 5791e30..d021d55 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__tsne.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__tsne.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + t-distributed stochastic neighbor embedding + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity tsne '$inputs' diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__umap.xml b/tools/suite_qiime2__diversity/qiime2__diversity__umap.xml index 13fe94b..a85ec88 100644 --- a/tools/suite_qiime2__diversity/qiime2__diversity__umap.xml +++ b/tools/suite_qiime2__diversity/qiime2__diversity__umap.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Uniform Manifold Approximation and Projection + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity q2galaxy run diversity umap '$inputs' diff --git a/tools/suite_qiime2__diversity/test-data/alpha_correlation.test0.alpha-div-faith-pd.qza b/tools/suite_qiime2__diversity/test-data/alpha_correlation.test0.alpha-div-faith-pd.qza index fc2d002..446ff91 100644 Binary files a/tools/suite_qiime2__diversity/test-data/alpha_correlation.test0.alpha-div-faith-pd.qza and b/tools/suite_qiime2__diversity/test-data/alpha_correlation.test0.alpha-div-faith-pd.qza differ diff --git a/tools/suite_qiime2__diversity/test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza b/tools/suite_qiime2__diversity/test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza index fc2d002..446ff91 100644 Binary files a/tools/suite_qiime2__diversity/test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza and b/tools/suite_qiime2__diversity/test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza differ diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__alpha_passthrough.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__alpha_passthrough.xml index 7f1022b..a2eb456 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__alpha_passthrough.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__alpha_passthrough.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Alpha Passthrough (non-phylogenetic) + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity_lib q2galaxy run diversity_lib alpha_passthrough '$inputs' diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_passthrough.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_passthrough.xml index 19798e4..4481037 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_passthrough.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_passthrough.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta Passthrough (non-phylogenetic) + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity_lib q2galaxy run diversity_lib beta_passthrough '$inputs' diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml index d02503c..ddb26ac 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta Phylogenetic Meta Passthrough + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity_lib q2galaxy run diversity_lib beta_phylogenetic_meta_passthrough '$inputs' diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml index 5e997af..7d018f5 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Beta Phylogenetic Passthrough + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity_lib q2galaxy run diversity_lib beta_phylogenetic_passthrough '$inputs' diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__bray_curtis.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__bray_curtis.xml index c2263e7..14805d7 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__bray_curtis.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__bray_curtis.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Bray-Curtis Dissimilarity + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity_lib q2galaxy run diversity_lib bray_curtis '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__faith_pd.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__faith_pd.xml index 7ed8997..f703351 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__faith_pd.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__faith_pd.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Faith's Phylogenetic Diversity + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity_lib q2galaxy run diversity_lib faith_pd '$inputs' @@ -23,9 +26,9 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__jaccard.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__jaccard.xml index 1612a95..c48b663 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__jaccard.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__jaccard.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Jaccard Distance + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity_lib q2galaxy run diversity_lib jaccard '$inputs' @@ -23,9 +26,9 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__observed_features.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__observed_features.xml index bdea044..646d150 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__observed_features.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__observed_features.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Observed Features + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity_lib q2galaxy run diversity_lib observed_features '$inputs' @@ -23,9 +26,9 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__pielou_evenness.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__pielou_evenness.xml index 310ba7d..00a34b8 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__pielou_evenness.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__pielou_evenness.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Pielou's Evenness + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity_lib q2galaxy run diversity_lib pielou_evenness '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__shannon_entropy.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__shannon_entropy.xml index de8973c..623559d 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__shannon_entropy.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__shannon_entropy.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Shannon's Entropy + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity_lib q2galaxy run diversity_lib shannon_entropy '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__unweighted_unifrac.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__unweighted_unifrac.xml index 422ca0a..a32b2d4 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__unweighted_unifrac.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__unweighted_unifrac.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Unweighted Unifrac + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity_lib q2galaxy run diversity_lib unweighted_unifrac '$inputs' @@ -23,9 +26,9 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__weighted_unifrac.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__weighted_unifrac.xml index 1ce3800..a142855 100644 --- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__weighted_unifrac.xml +++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__weighted_unifrac.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Weighted Unifrac + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version diversity_lib q2galaxy run diversity_lib weighted_unifrac '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__diversity_lib/test-data/alpha_passthrough.test0.feature-table.qza b/tools/suite_qiime2__diversity_lib/test-data/alpha_passthrough.test0.feature-table.qza index 8bfad11..20e1403 100644 Binary files a/tools/suite_qiime2__diversity_lib/test-data/alpha_passthrough.test0.feature-table.qza and b/tools/suite_qiime2__diversity_lib/test-data/alpha_passthrough.test0.feature-table.qza differ diff --git a/tools/suite_qiime2__diversity_lib/test-data/beta_passthrough.test0.feature-table.qza b/tools/suite_qiime2__diversity_lib/test-data/beta_passthrough.test0.feature-table.qza index 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b/tools/suite_qiime2__diversity_lib/test-data/weighted_unifrac.test3.phylogeny.qza differ diff --git a/tools/suite_qiime2__emperor/.shed.yml b/tools/suite_qiime2__emperor/.shed.yml index 8e10a6f..2bcb950 100644 --- a/tools/suite_qiime2__emperor/.shed.yml +++ b/tools/suite_qiime2__emperor/.shed.yml @@ -1,6 +1,6 @@ owner: q2d2 type: unrestricted -homepage_url: http://emperor.microbio.me +homepage_url: http://biocore.github.io/emperor/build/html/index.html remote_repository_url: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor categories: - Metagenomics diff --git a/tools/suite_qiime2__emperor/qiime2__emperor__biplot.xml b/tools/suite_qiime2__emperor/qiime2__emperor__biplot.xml index 398f87c..d713ed8 100644 --- a/tools/suite_qiime2__emperor/qiime2__emperor__biplot.xml +++ b/tools/suite_qiime2__emperor/qiime2__emperor__biplot.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Visualize and Interact with Principal Coordinates Analysis Biplot + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version emperor q2galaxy run emperor biplot '$inputs' diff --git a/tools/suite_qiime2__emperor/qiime2__emperor__plot.xml b/tools/suite_qiime2__emperor/qiime2__emperor__plot.xml index b205021..9ad7755 100644 --- a/tools/suite_qiime2__emperor/qiime2__emperor__plot.xml +++ b/tools/suite_qiime2__emperor/qiime2__emperor__plot.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Visualize and Interact with Principal Coordinates Analysis Plots + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version emperor q2galaxy run emperor plot '$inputs' diff --git a/tools/suite_qiime2__emperor/qiime2__emperor__procrustes_plot.xml b/tools/suite_qiime2__emperor/qiime2__emperor__procrustes_plot.xml index dbec522..4271478 100644 --- a/tools/suite_qiime2__emperor/qiime2__emperor__procrustes_plot.xml +++ b/tools/suite_qiime2__emperor/qiime2__emperor__procrustes_plot.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Visualize and Interact with a procrustes plot + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version emperor q2galaxy run emperor procrustes_plot '$inputs' diff --git a/tools/suite_qiime2__emperor/test-data/plot.test0.pcoa-result.qza b/tools/suite_qiime2__emperor/test-data/plot.test0.pcoa-result.qza index dff5a9f..b6d45e6 100644 Binary files a/tools/suite_qiime2__emperor/test-data/plot.test0.pcoa-result.qza and b/tools/suite_qiime2__emperor/test-data/plot.test0.pcoa-result.qza differ diff --git a/tools/suite_qiime2__emperor/test-data/procrustes_plot.test0.bc-pcoa-result.qza b/tools/suite_qiime2__emperor/test-data/procrustes_plot.test0.bc-pcoa-result.qza index dff5a9f..b6d45e6 100644 Binary files a/tools/suite_qiime2__emperor/test-data/procrustes_plot.test0.bc-pcoa-result.qza and b/tools/suite_qiime2__emperor/test-data/procrustes_plot.test0.bc-pcoa-result.qza differ diff --git a/tools/suite_qiime2__emperor/test-data/procrustes_plot.test0.unw-pcoa-result.qza b/tools/suite_qiime2__emperor/test-data/procrustes_plot.test0.unw-pcoa-result.qza index e92f74f..380572c 100644 Binary files a/tools/suite_qiime2__emperor/test-data/procrustes_plot.test0.unw-pcoa-result.qza and b/tools/suite_qiime2__emperor/test-data/procrustes_plot.test0.unw-pcoa-result.qza differ diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__blast.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__blast.xml index 345355e..9a69654 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__blast.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__blast.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + BLAST+ local alignment search. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_classifier q2galaxy run feature_classifier blast '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_blast.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_blast.xml index da94003..8849b10 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_blast.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_blast.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + BLAST+ consensus taxonomy classifier + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_classifier q2galaxy run feature_classifier classify_consensus_blast '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_vsearch.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_vsearch.xml index eb3df71..1ee36f1 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_vsearch.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_vsearch.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + VSEARCH-based consensus taxonomy classifier + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_classifier q2galaxy run feature_classifier classify_consensus_vsearch '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn.xml index de721ae..95b6c0c 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_classifier q2galaxy run feature_classifier classify_hybrid_vsearch_sklearn '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_sklearn.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_sklearn.xml index 0be630c..4424f4d 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_sklearn.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_sklearn.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Pre-fitted sklearn-based taxonomy classifier + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_classifier q2galaxy run feature_classifier classify_sklearn '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__extract_reads.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__extract_reads.xml index 3b42829..2fcc749 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__extract_reads.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__extract_reads.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Extract reads from reference sequences. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_classifier q2galaxy run feature_classifier extract_reads '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__find_consensus_annotation.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__find_consensus_annotation.xml index f7ba608..ff88bd6 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__find_consensus_annotation.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__find_consensus_annotation.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Find consensus among multiple annotations. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_classifier q2galaxy run feature_classifier find_consensus_annotation '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_naive_bayes.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_naive_bayes.xml index 512fdd3..c2f515d 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_naive_bayes.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_naive_bayes.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Train the naive_bayes classifier + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_classifier q2galaxy run feature_classifier fit_classifier_naive_bayes '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_sklearn.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_sklearn.xml index 24bdd23..92441a7 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_sklearn.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_sklearn.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Train an almost arbitrary scikit-learn classifier + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_classifier q2galaxy run feature_classifier fit_classifier_sklearn '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__makeblastdb.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__makeblastdb.xml index 6baad1b..838cf13 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__makeblastdb.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__makeblastdb.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Make BLAST database. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_classifier q2galaxy run feature_classifier makeblastdb '$inputs' diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__vsearch_global.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__vsearch_global.xml index b389d34..236295f 100644 --- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__vsearch_global.xml +++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__vsearch_global.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + VSEARCH global alignment search + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_classifier q2galaxy run feature_classifier vsearch_global '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__core_features.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__core_features.xml index 200afcf..769ab0f 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__core_features.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__core_features.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Identify core features in table + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table core_features '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features.xml index 30b1edf..4f755f3 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter features from table + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table filter_features '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features_conditionally.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features_conditionally.xml index e5579b1..973d7c5 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features_conditionally.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features_conditionally.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter features from a table based on abundance and prevalence + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table filter_features_conditionally '$inputs' @@ -23,9 +26,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_samples.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_samples.xml index 586f571..0ca6aae 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_samples.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_samples.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter samples from table + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table filter_samples '$inputs' @@ -23,9 +26,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_seqs.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_seqs.xml index 2395407..9205743 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_seqs.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_seqs.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter features from sequences + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table filter_seqs '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__group.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__group.xml index e7db53c..11a4074 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__group.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__group.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Group samples or features by a metadata column + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table group '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__heatmap.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__heatmap.xml index d991356..7b7a39e 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__heatmap.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__heatmap.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Generate a heatmap representation of a feature table + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table heatmap '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge.xml index 37476b7..82a3a6b 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Combine multiple tables + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table merge '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_seqs.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_seqs.xml index 0d2933b..85dae0f 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_seqs.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_seqs.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Combine collections of feature sequences + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table merge_seqs '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_taxa.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_taxa.xml index 6180bae..7f2f7fa 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_taxa.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_taxa.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Combine collections of feature taxonomies + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table merge_taxa '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__presence_absence.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__presence_absence.xml index 033a85d..d861861 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__presence_absence.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__presence_absence.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Convert to presence/absence + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table presence_absence '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__rarefy.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__rarefy.xml index 97cc068..8b0ae44 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__rarefy.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__rarefy.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Rarefy table + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table rarefy '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__relative_frequency.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__relative_frequency.xml index c5ae1af..9e0f25d 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__relative_frequency.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__relative_frequency.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Convert to relative frequencies + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table relative_frequency '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__rename_ids.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__rename_ids.xml index c4492a1..939c6d1 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__rename_ids.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__rename_ids.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Renames sample or feature ids in a table + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table rename_ids '$inputs' @@ -23,9 +26,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__split.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__split.xml index 237046b..5c6d1dd 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__split.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__split.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Split one feature table into many + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table split '$inputs' @@ -23,9 +26,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__subsample_ids.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__subsample_ids.xml index ebbc4a9..ced3a85 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__subsample_ids.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__subsample_ids.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Subsample table + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table subsample_ids '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize.xml index bbec807..5a777e6 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Summarize table + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table summarize '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize_plus.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize_plus.xml index ba84ae7..5dc8d5f 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize_plus.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize_plus.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Summarize table plus + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table summarize_plus '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_feature_frequencies.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_feature_frequencies.xml index edd0a2d..e7e6b3a 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_feature_frequencies.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_feature_frequencies.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Tabulate feature frequencies + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table tabulate_feature_frequencies '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_sample_frequencies.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_sample_frequencies.xml index 6952847..9fc2413 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_sample_frequencies.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_sample_frequencies.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Tabulate sample frequencies + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table tabulate_sample_frequencies '$inputs' diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_seqs.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_seqs.xml index a9b200a..a8ac1e9 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_seqs.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_seqs.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + View sequence associated with each feature + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table tabulate_seqs '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]'] diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__transpose.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__transpose.xml index af6a5d1..c145049 100644 --- a/tools/suite_qiime2__feature_table/qiime2__feature_table__transpose.xml +++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__transpose.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Transpose a feature table. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version feature_table q2galaxy run feature_table transpose '$inputs' @@ -23,9 +26,9 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__feature_table/test-data/filter_features.test0.feature-table.qza b/tools/suite_qiime2__feature_table/test-data/filter_features.test0.feature-table.qza index fe7827a..8e95dea 100644 Binary files a/tools/suite_qiime2__feature_table/test-data/filter_features.test0.feature-table.qza and b/tools/suite_qiime2__feature_table/test-data/filter_features.test0.feature-table.qza differ diff --git a/tools/suite_qiime2__feature_table/test-data/filter_features_conditionally.test0.feature-table.qza 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(SPDX: BSD-3-Clause) --> - + Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version fragment_insertion q2galaxy run fragment_insertion classify_otus_experimental '$inputs' diff --git a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__filter_features.xml b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__filter_features.xml index fdd6c4f..75915f0 100644 --- a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__filter_features.xml +++ b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__filter_features.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter fragments in tree from table. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version fragment_insertion q2galaxy run fragment_insertion filter_features '$inputs' diff --git a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__sepp.xml b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__sepp.xml index 305b00c..a6eb3e2 100644 --- a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__sepp.xml +++ b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__sepp.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Insert fragment sequences using SEPP into reference phylogenies. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version fragment_insertion q2galaxy run fragment_insertion sepp '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__anova.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__anova.xml index 2eea975..0cd9a55 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__anova.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__anova.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + ANOVA test + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version longitudinal q2galaxy run longitudinal anova '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__feature_volatility.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__feature_volatility.xml index df09824..83ad6ca 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__feature_volatility.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__feature_volatility.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Feature volatility analysis + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version longitudinal q2galaxy run longitudinal feature_volatility '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_differences.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_differences.xml index 9ad840e..8317a37 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_differences.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_differences.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Compute first differences or difference from baseline between sequential states + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version longitudinal q2galaxy run longitudinal first_differences '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_distances.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_distances.xml index 7355df3..c1014fe 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_distances.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_distances.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Compute first distances or distance from baseline between sequential states + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version longitudinal q2galaxy run longitudinal first_distances '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__linear_mixed_effects.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__linear_mixed_effects.xml index e477dce..7f03311 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__linear_mixed_effects.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__linear_mixed_effects.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Linear mixed effects modeling + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version longitudinal q2galaxy run longitudinal linear_mixed_effects '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__maturity_index.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__maturity_index.xml index 021ada8..a83260b 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__maturity_index.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__maturity_index.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Microbial maturity index prediction. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version longitudinal q2galaxy run longitudinal maturity_index '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__nmit.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__nmit.xml index fb2e70a..dcda23d 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__nmit.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__nmit.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Nonparametric microbial interdependence test + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version longitudinal q2galaxy run longitudinal nmit '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_differences.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_differences.xml index 75673f9..075b6da 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_differences.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_differences.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Paired difference testing and boxplots + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version longitudinal q2galaxy run longitudinal pairwise_differences '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_distances.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_distances.xml index d5884c7..e5eee3a 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_distances.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_distances.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Paired pairwise distance testing and boxplots + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version longitudinal q2galaxy run longitudinal pairwise_distances '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__plot_feature_volatility.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__plot_feature_volatility.xml index 39dd861..c9c373a 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__plot_feature_volatility.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__plot_feature_volatility.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Plot longitudinal feature volatility and importances + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version longitudinal q2galaxy run longitudinal plot_feature_volatility '$inputs' diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__volatility.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__volatility.xml index 8befde4..555adfb 100644 --- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__volatility.xml +++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__volatility.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Generate interactive volatility plot + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version longitudinal q2galaxy run longitudinal volatility '$inputs' diff --git a/tools/suite_qiime2__metadata/qiime2__metadata__distance_matrix.xml b/tools/suite_qiime2__metadata/qiime2__metadata__distance_matrix.xml index 589f86a..60073db 100644 --- a/tools/suite_qiime2__metadata/qiime2__metadata__distance_matrix.xml +++ b/tools/suite_qiime2__metadata/qiime2__metadata__distance_matrix.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Create a distance matrix from a numeric Metadata column + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version metadata q2galaxy run metadata distance_matrix '$inputs' diff --git a/tools/suite_qiime2__metadata/qiime2__metadata__merge.xml b/tools/suite_qiime2__metadata/qiime2__metadata__merge.xml index 9828c71..3c9ad4c 100644 --- a/tools/suite_qiime2__metadata/qiime2__metadata__merge.xml +++ b/tools/suite_qiime2__metadata/qiime2__metadata__merge.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Merge metadata + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version metadata q2galaxy run metadata merge '$inputs' diff --git a/tools/suite_qiime2__metadata/qiime2__metadata__shuffle_groups.xml b/tools/suite_qiime2__metadata/qiime2__metadata__shuffle_groups.xml index 520503d..3b4c6af 100644 --- a/tools/suite_qiime2__metadata/qiime2__metadata__shuffle_groups.xml +++ b/tools/suite_qiime2__metadata/qiime2__metadata__shuffle_groups.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Shuffle values in a categorical sample metadata column. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version metadata q2galaxy run metadata shuffle_groups '$inputs' diff --git a/tools/suite_qiime2__metadata/qiime2__metadata__tabulate.xml b/tools/suite_qiime2__metadata/qiime2__metadata__tabulate.xml index 681011f..0f088d4 100644 --- a/tools/suite_qiime2__metadata/qiime2__metadata__tabulate.xml +++ b/tools/suite_qiime2__metadata/qiime2__metadata__tabulate.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Interactively explore Metadata in an HTML table + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version metadata q2galaxy run metadata tabulate '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml index 6920f04..462e181 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Build a phylogenetic tree using fasttree and mafft alignment + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version phylogeny q2galaxy run phylogeny align_to_tree_mafft_fasttree '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml index 965ae0c..fa4bff5 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Build a phylogenetic tree using iqtree and mafft alignment. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version phylogeny q2galaxy run phylogeny align_to_tree_mafft_iqtree '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_raxml.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_raxml.xml index 5e6430b..214dcbb 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_raxml.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_raxml.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Build a phylogenetic tree using raxml and mafft alignment. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version phylogeny q2galaxy run phylogeny align_to_tree_mafft_raxml '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__fasttree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__fasttree.xml index 6975235..3469532 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__fasttree.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__fasttree.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Construct a phylogenetic tree with FastTree. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version phylogeny q2galaxy run phylogeny fasttree '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_table.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_table.xml index 3fdebc8..038887a 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_table.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_table.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Remove features from table if they're not present in tree. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version phylogeny q2galaxy run phylogeny filter_table '$inputs' @@ -23,16 +26,16 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]', 'Phylogeny[Unrooted]'] diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_tree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_tree.xml index 37c4ddb..e03bdaf 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_tree.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_tree.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Remove features from tree based on metadata + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version phylogeny q2galaxy run phylogeny filter_tree '$inputs' @@ -23,18 +26,18 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]', 'Phylogeny[Unrooted]']
- - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree.xml index c7a471e..0be76e1 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Construct a phylogenetic tree with IQ-TREE. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version phylogeny q2galaxy run phylogeny iqtree '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml index 87eaf54..344516e 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Construct a phylogenetic tree with IQ-TREE with bootstrap supports. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version phylogeny q2galaxy run phylogeny iqtree_ultrafast_bootstrap '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__midpoint_root.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__midpoint_root.xml index e0705f6..376e14a 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__midpoint_root.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__midpoint_root.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Midpoint root an unrooted phylogenetic tree. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version phylogeny q2galaxy run phylogeny midpoint_root '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml.xml index 1c74fc4..dc3a864 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Construct a phylogenetic tree with RAxML. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version phylogeny q2galaxy run phylogeny raxml '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml_rapid_bootstrap.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml_rapid_bootstrap.xml index e754fe9..c3612fa 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml_rapid_bootstrap.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml_rapid_bootstrap.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Construct a phylogenetic tree with bootstrap supports using RAxML. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version phylogeny q2galaxy run phylogeny raxml_rapid_bootstrap '$inputs' diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__robinson_foulds.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__robinson_foulds.xml index 73e0e98..6b6cb9f 100644 --- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__robinson_foulds.xml +++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__robinson_foulds.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Calculate Robinson-Foulds distance between phylogenetic trees. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version phylogeny q2galaxy run phylogeny robinson_foulds '$inputs' @@ -23,8 +26,8 @@ for: - +
diff --git a/tools/suite_qiime2__phylogeny/test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza b/tools/suite_qiime2__phylogeny/test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza index d7bf4be..174fb3c 100644 Binary files a/tools/suite_qiime2__phylogeny/test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza and b/tools/suite_qiime2__phylogeny/test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza differ diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__bowtie2_build.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__bowtie2_build.xml index 4ec016a..8b9451e 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__bowtie2_build.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__bowtie2_build.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Build bowtie2 index from reference sequences. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version quality_control q2galaxy run quality_control bowtie2_build '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify.xml index ab01781..be79d66 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Identify contaminants + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version quality_control q2galaxy run quality_control decontam_identify '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify_batches.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify_batches.xml index c05c83b..5badaee 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify_batches.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify_batches.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Identify contaminants in Batch Mode + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version quality_control q2galaxy run quality_control decontam_identify_batches '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_remove.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_remove.xml index 02a62e2..b2f4011 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_remove.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_remove.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Remove contaminants + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version quality_control q2galaxy run quality_control decontam_remove '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_score_viz.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_score_viz.xml index 73ec91b..33c2644 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_score_viz.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_score_viz.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Generate a histogram representation of the scores + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version quality_control q2galaxy run quality_control decontam_score_viz '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_composition.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_composition.xml index 411d05e..d0dc9c7 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_composition.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_composition.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Evaluate expected vs. observed taxonomic composition of samples + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version quality_control q2galaxy run quality_control evaluate_composition '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_seqs.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_seqs.xml index a1cb643..66a43ed 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_seqs.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_seqs.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Compare query (observed) vs. reference (expected) sequences. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version quality_control q2galaxy run quality_control evaluate_seqs '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_taxonomy.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_taxonomy.xml index dce7e7b..e4152e8 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_taxonomy.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_taxonomy.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Evaluate expected vs. observed taxonomic assignments + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version quality_control q2galaxy run quality_control evaluate_taxonomy '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__exclude_seqs.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__exclude_seqs.xml index 2777a99..d59a0b3 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__exclude_seqs.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__exclude_seqs.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Exclude sequences by alignment + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version quality_control q2galaxy run quality_control exclude_seqs '$inputs' diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__filter_reads.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__filter_reads.xml index ec8f431..6638d56 100644 --- a/tools/suite_qiime2__quality_control/qiime2__quality_control__filter_reads.xml +++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__filter_reads.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter demultiplexed sequences by alignment to reference database. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version quality_control q2galaxy run quality_control filter_reads '$inputs' diff --git a/tools/suite_qiime2__quality_filter/qiime2__quality_filter__q_score.xml b/tools/suite_qiime2__quality_filter/qiime2__quality_filter__q_score.xml index 3a2fd72..09d4f11 100644 --- a/tools/suite_qiime2__quality_filter/qiime2__quality_filter__q_score.xml +++ b/tools/suite_qiime2__quality_filter/qiime2__quality_filter__q_score.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Quality filter based on sequence quality scores. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version quality_filter q2galaxy run quality_filter q_score '$inputs' diff --git a/tools/suite_qiime2__quality_filter/test-data/q_score.test0.demuxed-seqs.qza b/tools/suite_qiime2__quality_filter/test-data/q_score.test0.demuxed-seqs.qza index 9a7b159..08286b3 100644 Binary files a/tools/suite_qiime2__quality_filter/test-data/q_score.test0.demuxed-seqs.qza and b/tools/suite_qiime2__quality_filter/test-data/q_score.test0.demuxed-seqs.qza differ diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__cull_seqs.xml b/tools/suite_qiime2__rescript/qiime2__rescript__cull_seqs.xml index bcd6168..e9ad8d7 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__cull_seqs.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__cull_seqs.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Removes sequences that contain at least the specified number of degenerate bases and/or homopolymers of a given length. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript cull_seqs '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[RNASequence]', 'FeatureData[Sequence]'] diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__degap_seqs.xml b/tools/suite_qiime2__rescript/qiime2__rescript__degap_seqs.xml index 06584eb..49ecacb 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__degap_seqs.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__degap_seqs.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Remove gaps from DNA sequence alignments. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript degap_seqs '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__dereplicate.xml b/tools/suite_qiime2__rescript/qiime2__rescript__dereplicate.xml index f30a80a..ad354bb 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__dereplicate.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__dereplicate.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Dereplicate features with matching sequences and taxonomies. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript dereplicate '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__edit_taxonomy.xml b/tools/suite_qiime2__rescript/qiime2__rescript__edit_taxonomy.xml index 5b14e24..adaad50 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__edit_taxonomy.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__edit_taxonomy.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Edit taxonomy strings with find and replace terms. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript edit_taxonomy '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_classifications.xml b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_classifications.xml index 49a227c..f8bab2c 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_classifications.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_classifications.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Interactively evaluate taxonomic classification accuracy. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript evaluate_classifications '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_cross_validate.xml b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_cross_validate.xml index a435750..937d2f1 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_cross_validate.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_cross_validate.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Evaluate DNA sequence reference database via cross-validated taxonomic classification. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript evaluate_cross_validate '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_fit_classifier.xml b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_fit_classifier.xml index 7991f17..cf96c54 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_fit_classifier.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_fit_classifier.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Evaluate and train naive Bayes classifier on reference sequences. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript evaluate_fit_classifier '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_seqs.xml b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_seqs.xml index 8dce81f..7311979 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_seqs.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_seqs.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Compute summary statistics on sequence artifact(s). + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript evaluate_seqs '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_taxonomy.xml b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_taxonomy.xml index 2956f37..cb01955 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_taxonomy.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__evaluate_taxonomy.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Compute summary statistics on taxonomy artifact(s). + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript evaluate_taxonomy '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__extract_seq_segments.xml b/tools/suite_qiime2__rescript/qiime2__rescript__extract_seq_segments.xml index 97521c5..c5c9254 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__extract_seq_segments.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__extract_seq_segments.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined 'perc-identity' value. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript extract_seq_segments '$inputs' @@ -27,7 +30,7 @@ for: hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]'] - + @@ -35,6 +38,7 @@ for:
+
diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length.xml b/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length.xml index f517cce..9cfd76e 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter sequences by length. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript filter_seqs_length '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length_by_taxon.xml b/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length_by_taxon.xml index dc0dc6d..2bf9cf7 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length_by_taxon.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__filter_seqs_length_by_taxon.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter sequences by length and taxonomic group. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript filter_seqs_length_by_taxon '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__filter_taxa.xml b/tools/suite_qiime2__rescript/qiime2__rescript__filter_taxa.xml index a7d829b..0cfadf4 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__filter_taxa.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__filter_taxa.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Filter taxonomy by list of IDs or search criteria. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript filter_taxa '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_bv_brc_genome_features.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_bv_brc_genome_features.xml new file mode 100644 index 0000000..56c666e --- /dev/null +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_bv_brc_genome_features.xml @@ -0,0 +1,172 @@ + + + + + Fetch genome features from BV-BRC. + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version rescript + q2galaxy run rescript get_bv_brc_genome_features '$inputs' + + + + +
+ + + + + + + + + + + value != "1" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + value is not None and len(value) > 0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + value != '__q2galaxy__::literal::None' + + + +
+ + + + + + + + + +QIIME 2: rescript get-bv-brc-genome-features +============================================ +Fetch genome features from BV-BRC. + + +Outputs: +-------- +:genes.qza: Gene +:proteins.qza: proteins +:taxonomy.qza: Taxonomy data for all sequences. +:loci.qza: loci + +| + +Description: +------------ +Fetch DNA and protein sequences of genome features from BV-BRC. BV-BRC (Bacterial and Viral Bioinformatics Resource Center) is a database for bacterial and viral genomes, annotations, and metadata. There are three ways to query data: You can use an RQL query to refine your search and get targeted features. By providing IDs/values and a corresponding data field, you can retrieve all features associated with those specific values in that data field. And as a third option a metadata column can be provided, to use metadata obtained with the action get-bv-brc-metadata as a new query. Check https://www.bv-brc.org/api/doc/ for documentation. + + +| + + + + @article{cite1, + author = {Olson, Robert D and Assaf, Rida and Brettin, Thomas and Conrad, Neal and Cucinell, Clark and Davis, James J and Dempsey, Donald M and Dickerman, Allan and Dietrich, Emily M and Kenyon, Ronald W and others}, + journal = {Nucleic acids research}, + number = {D1}, + pages = {D678--D689}, + publisher = {Oxford University Press}, + title = {Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR}, + volume = {51}, + year = {2023} +} + + 10.1371/journal.pcbi.1009581 + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_bv_brc_genomes.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_bv_brc_genomes.xml new file mode 100644 index 0000000..9831efc --- /dev/null +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_bv_brc_genomes.xml @@ -0,0 +1,168 @@ + + + + + Get genome sequences from the BV-BRC database. + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version rescript + q2galaxy run rescript get_bv_brc_genomes '$inputs' + + + + +
+ + + + + + + + + + + value != "1" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + value is not None and len(value) > 0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + value != '__q2galaxy__::literal::None' + + + +
+ + + + + + + +QIIME 2: rescript get-bv-brc-genomes +==================================== +Get genome sequences from the BV-BRC database. + + +Outputs: +-------- +:genomes.qza: Genome sequences for specified query. +:taxonomy.qza: Taxonomy data for all sequences. + +| + +Description: +------------ +Fetch genome sequences from BV-BRC. BV-BRC (Bacterial and Viral Bioinformatics Resource Center) is a database for bacterial and viral genomes, annotations, and metadata. There are three ways to query data: You can use an RQL query to refine your search and get targeted genomes. By providing IDs/values and a corresponding data field, you can retrieve all genomes associated with those specific values in that data field. And as a third option a metadata column can be provided, to use metadata obtained with the action get-bv-brc-metadata as a new query. Check https://www.bv-brc.org/api/doc/ for documentation. + + +| + + + + @article{cite1, + author = {Olson, Robert D and Assaf, Rida and Brettin, Thomas and Conrad, Neal and Cucinell, Clark and Davis, James J and Dempsey, Donald M and Dickerman, Allan and Dietrich, Emily M and Kenyon, Ronald W and others}, + journal = {Nucleic acids research}, + number = {D1}, + pages = {D678--D689}, + publisher = {Oxford University Press}, + title = {Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR}, + volume = {51}, + year = {2023} +} + + 10.1371/journal.pcbi.1009581 + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_bv_brc_metadata.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_bv_brc_metadata.xml new file mode 100644 index 0000000..0a9fdfb --- /dev/null +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_bv_brc_metadata.xml @@ -0,0 +1,166 @@ + + + + + Fetch BV-BCR metadata. + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version rescript + q2galaxy run rescript get_bv_brc_metadata '$inputs' + + + + +
+ + + + + + + + + + + value != "1" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + value is not None and len(value) > 0 + + +
+ + + + + + +QIIME 2: rescript get-bv-brc-metadata +===================================== +Fetch BV-BCR metadata. + + +Outputs: +-------- +:metadata.qza: BV-BCR metadata of specified data type. + +| + +Description: +------------ +Fetch BV-BCR metadata for a specific data type. BV-BRC (Bacterial and Viral Bioinformatics Resource Center) is a database for bacterial and viral genomes, annotations, and metadata. There are three ways to query data: You can use an RQL query to refine your search and get targeted results. By providing IDs/values and a corresponding data field, you can retrieve all metadata associated with those specific values in that data field. And as a third option a metadata column can be provided, to use the results from other data types as a new query. Check https://www.bv-brc.org/api/doc/ for documentation. + + +| + + + + @article{cite1, + author = {Olson, Robert D and Assaf, Rida and Brettin, Thomas and Conrad, Neal and Cucinell, Clark and Davis, James J and Dempsey, Donald M and Dickerman, Allan and Dietrich, Emily M and Kenyon, Ronald W and others}, + journal = {Nucleic acids research}, + number = {D1}, + pages = {D678--D689}, + publisher = {Oxford University Press}, + title = {Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR}, + volume = {51}, + year = {2023} +} + + 10.1371/journal.pcbi.1009581 + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_gtdb_data.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_gtdb_data.xml index b77d01f..3d60a25 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__get_gtdb_data.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_gtdb_data.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Download, parse, and import SSU GTDB reference data. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript get_gtdb_data '$inputs' @@ -22,11 +25,12 @@ for:
- + - + + diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data.xml index 3562e7f..aa85b7d 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Download, parse, and import NCBI sequences and taxonomies + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript get_ncbi_data '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data_protein.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data_protein.xml index e4877b6..23d197d 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data_protein.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_data_protein.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Download, parse, and import NCBI protein sequences and taxonomies + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript get_ncbi_data_protein '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_genomes.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_genomes.xml index 350c0c5..dd539bf 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_genomes.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_ncbi_genomes.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript get_ncbi_genomes '$inputs' @@ -28,9 +31,10 @@ for: value is not None and len(value) > 0
- + + @@ -43,8 +47,46 @@ for: + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + value != '__q2galaxy__::literal::None' + + +
diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_silva_data.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_silva_data.xml index 9a1840d..de66ec7 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__get_silva_data.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_silva_data.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Download, parse, and import SILVA database. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript get_silva_data '$inputs' @@ -22,11 +25,12 @@ for:
- + - + + diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__get_unite_data.xml b/tools/suite_qiime2__rescript/qiime2__rescript__get_unite_data.xml index fcea920..064eed7 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__get_unite_data.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__get_unite_data.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Download and import UNITE reference data. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript get_unite_data '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__merge_taxa.xml b/tools/suite_qiime2__rescript/qiime2__rescript__merge_taxa.xml index b1a5f09..efa79de 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__merge_taxa.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__merge_taxa.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Compare taxonomies and select the longest, highest scoring, or find the least common ancestor. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript merge_taxa '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__orient_seqs.xml b/tools/suite_qiime2__rescript/qiime2__rescript__orient_seqs.xml index 12ed70e..656b2a9 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__orient_seqs.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__orient_seqs.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Orient input sequences by comparison against reference. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript orient_seqs '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__parse_silva_taxonomy.xml b/tools/suite_qiime2__rescript/qiime2__rescript__parse_silva_taxonomy.xml index af2a48c..44dfe71 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__parse_silva_taxonomy.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__parse_silva_taxonomy.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Generates a SILVA fixed-rank taxonomy. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript parse_silva_taxonomy '$inputs' diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__reverse_transcribe.xml b/tools/suite_qiime2__rescript/qiime2__rescript__reverse_transcribe.xml index 4318645..d7803c4 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__reverse_transcribe.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__reverse_transcribe.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Reverse transcribe RNA to DNA sequences. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript reverse_transcribe '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedRNASequence]', 'FeatureData[RNASequence]'] diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__subsample_fasta.xml b/tools/suite_qiime2__rescript/qiime2__rescript__subsample_fasta.xml index a2e53d3..e6f6462 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__subsample_fasta.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__subsample_fasta.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Subsample an indicated number of sequences from a FASTA file. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript subsample_fasta '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]'] diff --git a/tools/suite_qiime2__rescript/qiime2__rescript__trim_alignment.xml b/tools/suite_qiime2__rescript/qiime2__rescript__trim_alignment.xml index 89f5183..1f92b78 100644 --- a/tools/suite_qiime2__rescript/qiime2__rescript__trim_alignment.xml +++ b/tools/suite_qiime2__rescript/qiime2__rescript__trim_alignment.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Trim alignment based on provided primers or specific positions. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version rescript q2galaxy run rescript trim_alignment '$inputs' @@ -29,7 +32,7 @@ for:
- + @@ -45,7 +48,7 @@ for: - + @@ -62,6 +65,7 @@ for: +
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples.xml index 05934de..ce32eab 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Train and test a cross-validated supervised learning classifier. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier classify_samples '$inputs' @@ -23,9 +26,9 @@ for: + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_from_dist.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_from_dist.xml index e5c4888..804b8c3 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_from_dist.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_from_dist.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Run k-nearest-neighbors on a labeled distance matrix. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier classify_samples_from_dist '$inputs' diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_ncv.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_ncv.xml index f3c9e3d..5960f40 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_ncv.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_ncv.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Nested cross-validated supervised learning classifier. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier classify_samples_ncv '$inputs' @@ -23,9 +26,9 @@ for: + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__confusion_matrix.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__confusion_matrix.xml index d3e43f4..d42728f 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__confusion_matrix.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__confusion_matrix.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Make a confusion matrix from sample classifier predictions. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier confusion_matrix '$inputs' diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_classifier.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_classifier.xml index 9f1b417..cb3b8d2 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_classifier.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_classifier.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Fit a supervised learning classifier. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier fit_classifier '$inputs' @@ -23,9 +26,9 @@ for: + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_regressor.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_regressor.xml index def7f2e..4db7297 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_regressor.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_regressor.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Fit a supervised learning regressor. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier fit_regressor '$inputs' @@ -23,9 +26,9 @@ for: + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__heatmap.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__heatmap.xml index 33cc6a7..1749804 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__heatmap.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__heatmap.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Generate heatmap of important features. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier heatmap '$inputs' @@ -23,9 +26,9 @@ for: + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__metatable.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__metatable.xml index c9660db..46ad628 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__metatable.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__metatable.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Convert (and merge) positive numeric metadata (in)to feature table. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier metatable '$inputs' @@ -38,9 +41,9 @@ for:
+ - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_classification.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_classification.xml index 3473243..52c8855 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_classification.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_classification.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Use trained classifier to predict target values for new samples. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier predict_classification '$inputs' @@ -23,9 +26,9 @@ for: + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_regression.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_regression.xml index 64cad4c..2d19a20 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_regression.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_regression.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Use trained regressor to predict target values for new samples. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier predict_regression '$inputs' @@ -23,9 +26,9 @@ for: + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples.xml index f852d95..ac95da1 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Train and test a cross-validated supervised learning regressor. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier regress_samples '$inputs' @@ -23,9 +26,9 @@ for: + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples_ncv.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples_ncv.xml index 0153d28..35b5dc2 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples_ncv.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples_ncv.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Nested cross-validated supervised learning regressor. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier regress_samples_ncv '$inputs' @@ -23,9 +26,9 @@ for: + - hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__scatterplot.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__scatterplot.xml index 40deb94..2d8ebb1 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__scatterplot.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__scatterplot.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Make 2D scatterplot and linear regression of regressor predictions. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier scatterplot '$inputs' diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__split_table.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__split_table.xml index fa4808f..7c7ddd5 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__split_table.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__split_table.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Split a feature table into training and testing sets. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier split_table '$inputs' @@ -23,12 +26,12 @@ for: - - + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Balance]', 'FeatureTable[Composition]', 'FeatureTable[Design]', 'FeatureTable[Frequency]', 'FeatureTable[PercentileNormalized]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__summarize.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__summarize.xml index 204ee37..6f0af46 100644 --- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__summarize.xml +++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__summarize.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Summarize parameter and feature extraction information for a trained estimator. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version sample_classifier q2galaxy run sample_classifier summarize '$inputs' @@ -23,8 +26,8 @@ for: - + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleEstimator[Classifier]', 'SampleEstimator[Regressor]'] diff --git a/tools/suite_qiime2__stats/.shed.yml b/tools/suite_qiime2__stats/.shed.yml new file mode 100644 index 0000000..639d5b0 --- /dev/null +++ b/tools/suite_qiime2__stats/.shed.yml @@ -0,0 +1,16 @@ +owner: q2d2 +type: unrestricted +homepage_url: https://github.com/qiime2/q2-stats +remote_repository_url: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats +categories: + - Metagenomics + - Sequence Analysis + - Statistics +auto_tool_repositories: + name_template: '{{ tool_id }}' + description_template: 'Galaxy tool for QIIME 2 action: ''{{tool_name}}''.' +suite: + name: suite_qiime2__stats + description: 'Galaxy suite for QIIME 2 plugin: ''stats''. Plugin for statistical + analyses.' + long_description: This QIIME 2 plugin supports statistical analyses. diff --git a/tools/suite_qiime2__stats/qiime2__stats__alpha_group_significance.xml b/tools/suite_qiime2__stats/qiime2__stats__alpha_group_significance.xml new file mode 100644 index 0000000..01dad82 --- /dev/null +++ b/tools/suite_qiime2__stats/qiime2__stats__alpha_group_significance.xml @@ -0,0 +1,268 @@ + + + + + Alpha group significance test and plot + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version stats + q2galaxy run stats alpha_group_significance '$inputs' + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[AlphaDiversity]'] + + + + + + + + + + + + + + + + + + + + + value is not None and len(value) > 0 + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +QIIME 2: stats alpha-group-significance +======================================= +Alpha group significance test and plot + + +Outputs: +-------- +:distribution.qza: Dist1D generated by metadata and alpha diversity. +:stats.qza: A stats table of the per-group/timepoint results +:raincloud.qzv: A visualization of the distribution and statistics + +| + +Description: +------------ +Will select between Wilcoxon SRT and Mann-Whitney U depending on the presence of repeated measures. + +Examples: +--------- + +alpha_group_significance_faith_pd +********************************* +Using the ``qiime2 stats alpha-group-significance`` tool: + #. Set *"alpha_diversity"* to ``#: alpha-div-faith-pd.qza`` + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. For *"columns"*, use the ``+ columns`` button to add the corresponding values: + + #. Add *"element"* set to ``genotype`` + #. Add *"element"* set to ``donor_status`` + + #. Expand the ``additional options`` section + + #. Set *"subject"* to ``mouse_id`` + #. Set *"timepoint"* to ``days_post_transplant`` + + #. Press the ``Execute`` button. + +Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 stats alpha-group-significance [...] : distribution.qza`` + - ``dist.qza`` + * - ``#: qiime2 stats alpha-group-significance [...] : stats.qza`` + - ``stats.qza`` + * - ``#: qiime2 stats alpha-group-significance [...] : raincloud.qzv`` + - ``raincloud.qzv`` + +Using the ``qiime2 stats alpha-group-significance`` tool: + #. Set *"alpha_diversity"* to ``#: alpha-div-faith-pd.qza`` + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. For *"columns"*, use the ``+ columns`` button to add the corresponding values: + + #. Add *"element"* set to ``genotype`` + #. Add *"element"* set to ``donor_status`` + + #. Press the ``Execute`` button. + +Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 stats alpha-group-significance [...] : distribution.qza`` + - ``dist2.qza`` + * - ``#: qiime2 stats alpha-group-significance [...] : stats.qza`` + - ``stats2.qza`` + * - ``#: qiime2 stats alpha-group-significance [...] : raincloud.qzv`` + - ``raincloud2.qzv`` + + +| + + + + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__stats/qiime2__stats__collate_stats.xml b/tools/suite_qiime2__stats/qiime2__stats__collate_stats.xml new file mode 100644 index 0000000..6e6b37b --- /dev/null +++ b/tools/suite_qiime2__stats/qiime2__stats__collate_stats.xml @@ -0,0 +1,60 @@ + + + + + Combine and FDR correct multiple stats + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version stats + q2galaxy run stats collate_stats '$inputs' + + + + + + + + + + + + + + + +QIIME 2: stats collate-stats +============================ +Combine and FDR correct multiple stats + + +Outputs: +-------- +:table.qza: <no description> + +| + +Description: +------------ +Converts a collection of stats tables into a single table + + +| + + + + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__stats/qiime2__stats__facet_across.xml b/tools/suite_qiime2__stats/qiime2__stats__facet_across.xml new file mode 100644 index 0000000..2399e56 --- /dev/null +++ b/tools/suite_qiime2__stats/qiime2__stats__facet_across.xml @@ -0,0 +1,66 @@ + + + + + Facet across outer group + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version stats + q2galaxy run stats facet_across '$inputs' + + + + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Dist1D[NestedOrdered, Independent]', 'Dist1D[NestedOrdered, Matched]', 'Dist1D[NestedUnordered, Independent]', 'Dist1D[NestedUnordered, Matched]'] + + + + + + + + + +QIIME 2: stats facet-across +=========================== +Facet across outer group + + +Outputs: +-------- +:distributions.qza: A collection of non-nested Dist1Ds + +| + +Description: +------------ +Facet a distribution into per-class/level distributions where each facet preserves the outer group structure. + + +| + + + + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__stats/qiime2__stats__facet_within.xml b/tools/suite_qiime2__stats/qiime2__stats__facet_within.xml new file mode 100644 index 0000000..99b1abb --- /dev/null +++ b/tools/suite_qiime2__stats/qiime2__stats__facet_within.xml @@ -0,0 +1,68 @@ + + + + + Facet within outer group + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version stats + q2galaxy run stats facet_within '$inputs' + + + + + + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Dist1D[Multi, Independent]', 'Dist1D[Multi, Matched]', 'Dist1D[NestedOrdered, Independent]', 'Dist1D[NestedOrdered, Matched]', 'Dist1D[NestedUnordered, Independent]', 'Dist1D[NestedUnordered, Matched]'] + + + + + + + + + +QIIME 2: stats facet-within +=========================== +Facet within outer group + + +Outputs: +-------- +:distributions.qza: A collection of unordered and independent Dist1Ds. + +| + +Description: +------------ +Facets a distribution into independent distributions where each facet is an inner slice from the outer group. + + +| + + + + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__stats/qiime2__stats__mann_whitney_u.xml b/tools/suite_qiime2__stats/qiime2__stats__mann_whitney_u.xml new file mode 100644 index 0000000..48baf4f --- /dev/null +++ b/tools/suite_qiime2__stats/qiime2__stats__mann_whitney_u.xml @@ -0,0 +1,136 @@ + + + + + Mann-Whitney U Test + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version stats + q2galaxy run stats mann_whitney_u '$inputs' + + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Dist1D[Ordered, Independent]', 'Dist1D[Unordered, Independent]'] + + + + + + value != '__q2galaxy__::literal::None' + +
+ + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Dist1D[Ordered, Independent]', 'Dist1D[Ordered, Matched]', 'Dist1D[Unordered, Independent]', 'Dist1D[Unordered, Matched]'] + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + +QIIME 2: stats mann-whitney-u +============================= +Mann-Whitney U Test + + +Outputs: +-------- +:stats.qza: The Mann-Whitney U table for either the "reference" or "all-pairwise" comparison. + +| + +Description: +------------ + + +Examples: +--------- + +mann_whitney_pairwise +********************* +Using the ``qiime2 stats mann-whitney-u`` tool: + #. Set *"distribution"* to ``#: refdist.qza`` + #. Set *"compare"* to ``all-pairwise`` + #. Expand the ``additional options`` section + + #. Set *"against_each"* to ``#: timedist.qza`` + #. Set *"p_val_approx"* to ``asymptotic`` + + #. Press the ``Execute`` button. + + + +| + + + + 10.1214/aoms/1177730491 + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__stats/qiime2__stats__mann_whitney_u_facet.xml b/tools/suite_qiime2__stats/qiime2__stats__mann_whitney_u_facet.xml new file mode 100644 index 0000000..b84ded6 --- /dev/null +++ b/tools/suite_qiime2__stats/qiime2__stats__mann_whitney_u_facet.xml @@ -0,0 +1,112 @@ + + + + + Per-facet Mann-Whitney U Test + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version stats + q2galaxy run stats mann_whitney_u_facet '$inputs' + + + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Dist1D[Multi, Independent]', 'Dist1D[NestedOrdered, Independent]', 'Dist1D[NestedOrdered, Matched]', 'Dist1D[NestedUnordered, Independent]', 'Dist1D[NestedUnordered, Matched]'] + +
+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +QIIME 2: stats mann-whitney-u-facet +=================================== +Per-facet Mann-Whitney U Test + + +Outputs: +-------- +:stats.qza: <no description> + +| + +Description: +------------ + + +Examples: +--------- + +mann_whitney_u_facet_across +*************************** +Using the ``qiime2 stats mann-whitney-u-facet`` tool: + #. Set *"distribution"* to ``#: dist.qza`` + #. Expand the ``additional options`` section + + - Set *"facet"* to ``across`` + + #. Press the ``Execute`` button. + + +mann_whitney_u_facet_within +*************************** +Using the ``qiime2 stats mann-whitney-u-facet`` tool: + #. Set *"distribution"* to ``#: dist.qza`` + #. Expand the ``additional options`` section + + - Leave *"facet"* as its default value of ``within`` + + #. Press the ``Execute`` button. + + + +| + + + + 10.1214/aoms/1177730491 + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__stats/qiime2__stats__plot_rainclouds.xml b/tools/suite_qiime2__stats/qiime2__stats__plot_rainclouds.xml new file mode 100644 index 0000000..b1ddda5 --- /dev/null +++ b/tools/suite_qiime2__stats/qiime2__stats__plot_rainclouds.xml @@ -0,0 +1,110 @@ + + + + + Raincloud plots + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version stats + q2galaxy run stats plot_rainclouds '$inputs' + + + + + + + + + + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Dist1D[Multi, Independent]', 'Dist1D[Multi, Matched]', 'Dist1D[NestedOrdered, Independent]', 'Dist1D[NestedOrdered, Matched]', 'Dist1D[NestedUnordered, Independent]', 'Dist1D[NestedUnordered, Matched]', 'Dist1D[Ordered, Independent]', 'Dist1D[Ordered, Matched]', 'Dist1D[Unordered, Independent]', 'Dist1D[Unordered, Matched]'] + +
+ + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['StatsTable[Pairwise]'] + +
+ + + + + + + + + + + + + + + + + +QIIME 2: stats plot-rainclouds +============================== +Raincloud plots + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Plot raincloud distributions for each group. + +Examples: +--------- + +plot_rainclouds +*************** +Using the ``qiime2 stats plot-rainclouds`` tool: + #. Set *"data"* to ``#: dist.qza`` + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 stats plot-rainclouds [...] : visualization.qzv`` + - ``raincloud-plot.qzv`` + + +| + + + + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__stats/qiime2__stats__prep_alpha_distribution.xml b/tools/suite_qiime2__stats/qiime2__stats__prep_alpha_distribution.xml new file mode 100644 index 0000000..10222c5 --- /dev/null +++ b/tools/suite_qiime2__stats/qiime2__stats__prep_alpha_distribution.xml @@ -0,0 +1,133 @@ + + + + + Alpha diversity to Dist1D + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version stats + q2galaxy run stats prep_alpha_distribution '$inputs' + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[AlphaDiversity]'] + + + + + + + + + + + + + + + + + + + + + value is not None and len(value) > 0 + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + +QIIME 2: stats prep-alpha-distribution +====================================== +Alpha diversity to Dist1D + + +Outputs: +-------- +:distribution.qza: The resulting Dist1D. + +| + +Description: +------------ +Alpha diversity to Dist1D + + +| + + + + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__stats/qiime2__stats__wilcoxon_srt.xml b/tools/suite_qiime2__stats/qiime2__stats__wilcoxon_srt.xml new file mode 100644 index 0000000..346555b --- /dev/null +++ b/tools/suite_qiime2__stats/qiime2__stats__wilcoxon_srt.xml @@ -0,0 +1,127 @@ + + + + + Wilcoxon Signed Rank Test + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version stats + q2galaxy run stats wilcoxon_srt '$inputs' + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Dist1D[Ordered, Matched]'] + + + + + + value != '__q2galaxy__::literal::None' + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + +QIIME 2: stats wilcoxon-srt +=========================== +Wilcoxon Signed Rank Test + + +Outputs: +-------- +:stats.qza: The Wilcoxon SRT table for either the "baseline" or "consecutive" comparison. + +| + +Description: +------------ + + +Examples: +--------- + +wilcoxon_baseline0 +****************** +Using the ``qiime2 stats wilcoxon-srt`` tool: + #. Set *"distribution"* to ``#: timedist.qza`` + #. Set *"compare"* to ``baseline`` + #. Expand the ``additional options`` section + + #. Set *"baseline_group"* to ``0`` + #. Set *"p_val_approx"* to ``asymptotic`` + + #. Press the ``Execute`` button. + + + +| + + + + https://doi.org/10.2307/3001968 + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__stats/qiime2__stats__wilcoxon_srt_facet.xml b/tools/suite_qiime2__stats/qiime2__stats__wilcoxon_srt_facet.xml new file mode 100644 index 0000000..fbb6a99 --- /dev/null +++ b/tools/suite_qiime2__stats/qiime2__stats__wilcoxon_srt_facet.xml @@ -0,0 +1,82 @@ + + + + + Per-facet Wilcoxon Signed Rank Test + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version stats + q2galaxy run stats wilcoxon_srt_facet '$inputs' + + + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Dist1D[Multi, Matched]', 'Dist1D[NestedOrdered, Matched]', 'Dist1D[NestedUnordered, Matched]'] + +
+ +
+ + + + + + + + + + + +QIIME 2: stats wilcoxon-srt-facet +================================= +Per-facet Wilcoxon Signed Rank Test + + +Outputs: +-------- +:stats.qza: <no description> + +| + +Description: +------------ + + +Examples: +--------- + +wilcoxon_srt_facet +****************** +Using the ``qiime2 stats wilcoxon-srt-facet`` tool: + #. Set *"distribution"* to ``#: dist.qza`` + #. Press the ``Execute`` button. + + + +| + + + + https://doi.org/10.2307/3001968 + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__stats/test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza b/tools/suite_qiime2__stats/test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza new file mode 100644 index 0000000..99f41ae Binary files /dev/null and b/tools/suite_qiime2__stats/test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza differ diff --git a/tools/suite_qiime2__stats/test-data/alpha_group_significance.test0.metadata.tsv b/tools/suite_qiime2__stats/test-data/alpha_group_significance.test0.metadata.tsv new file mode 100644 index 0000000..01028f5 --- /dev/null +++ b/tools/suite_qiime2__stats/test-data/alpha_group_significance.test0.metadata.tsv @@ -0,0 +1,50 @@ +sample_name barcode mouse_id genotype cage_id donor donor_status days_post_transplant genotype_and_donor_status +#q2:types categorical categorical categorical categorical categorical categorical numeric categorical +recip.220.WT.OB1.D7 CCTCCGTCATGG 457 wild type C35 hc_1 Healthy 49 wild type and Healthy +recip.290.ASO.OB2.D1 AACAGTAAACAA 456 susceptible C35 hc_1 Healthy 49 susceptible and Healthy +recip.389.WT.HC2.D21 ATGTATCAATTA 435 susceptible C31 hc_1 Healthy 21 susceptible and Healthy +recip.391.ASO.PD2.D14 GTCAGTATGGCT 435 susceptible C31 hc_1 Healthy 14 susceptible and Healthy +recip.391.ASO.PD2.D21 AGACAGTAGGAG 437 susceptible C31 hc_1 Healthy 21 susceptible and Healthy +recip.391.ASO.PD2.D7 GGTCTTAGCACC 435 susceptible C31 hc_1 Healthy 7 susceptible and Healthy +recip.400.ASO.HC2.D14 CGTTCGCTAGCC 437 susceptible C31 hc_1 Healthy 14 susceptible and Healthy +recip.401.ASO.HC2.D7 ATTTACAATTGA 437 susceptible C31 hc_1 Healthy 7 susceptible and Healthy +recip.403.ASO.PD2.D21 CGCAGATTAGTA 456 susceptible C35 hc_1 Healthy 21 susceptible and Healthy +recip.411.ASO.HC2.D14 ATGTTAGGGAAT 456 susceptible C35 hc_1 Healthy 14 susceptible and Healthy +recip.411.ASO.HC2.D21 CTCATATGCTAT 457 wild type C35 hc_1 Healthy 21 wild type and Healthy +recip.411.ASO.HC2.D49 GCAACGAACGAG 435 susceptible C31 hc_1 Healthy 49 susceptible and Healthy +recip.412.ASO.HC2.D14 AAGTGGCTATCC 457 wild type C35 hc_1 Healthy 14 wild type and Healthy +recip.412.ASO.HC2.D7 GCATTCGGCGTT 456 susceptible C35 hc_1 Healthy 7 susceptible and Healthy +recip.413.WT.HC2.D7 ACCAGTGACTCA 457 wild type C35 hc_1 Healthy 7 wild type and Healthy +recip.456.ASO.HC3.D49 ACGGCGTTATGT 468 wild type C42 hc_1 Healthy 49 wild type and Healthy +recip.458.ASO.HC3.D21 ACGGCCCTGGAG 468 wild type C42 hc_1 Healthy 21 wild type and Healthy +recip.458.ASO.HC3.D49 CATTTGACGACG 469 wild type C42 hc_1 Healthy 49 wild type and Healthy +recip.459.WT.HC3.D14 ACATGGGCGGAA 468 wild type C42 hc_1 Healthy 14 wild type and Healthy +recip.459.WT.HC3.D21 CATAAATTCTTG 469 wild type C42 hc_1 Healthy 21 wild type and Healthy +recip.459.WT.HC3.D49 GCTGCGTATACC 536 susceptible C43 pd_1 PD 49 susceptible and PD +recip.460.WT.HC3.D14 CTGCGGATATAC 469 wild type C42 hc_1 Healthy 14 wild type and Healthy +recip.460.WT.HC3.D21 GTCAATTAGTGG 536 susceptible C43 pd_1 PD 21 susceptible and PD +recip.460.WT.HC3.D49 GAGAAGCTTATA 537 wild type C43 pd_1 PD 49 wild type and PD +recip.460.WT.HC3.D7 GACCCGTTTCGC 468 wild type C42 hc_1 Healthy 7 wild type and Healthy +recip.461.ASO.HC3.D21 AGCCCGCAAAGG 537 wild type C43 pd_1 PD 21 wild type and PD +recip.461.ASO.HC3.D49 GGCGTAACGGCA 538 wild type C44 pd_1 PD 49 wild type and PD +recip.461.ASO.HC3.D7 ATTGCCTTGATT 469 wild type C42 hc_1 Healthy 7 wild type and Healthy +recip.462.WT.PD3.D14 GTGAGGGCAAGT 536 susceptible C43 pd_1 PD 14 susceptible and PD +recip.462.WT.PD3.D21 GGCCTATAAGTC 538 wild type C44 pd_1 PD 21 wild type and PD +recip.462.WT.PD3.D49 AATACAGACCTG 539 susceptible C44 pd_1 PD 49 susceptible and PD +recip.462.WT.PD3.D7 TTAGGATTCTAT 536 susceptible C43 pd_1 PD 7 susceptible and PD +recip.463.WT.PD3.D14 ATATTGGCAGCC 537 wild type C43 pd_1 PD 14 wild type and PD +recip.463.WT.PD3.D21 CGCGGCGCAGCT 539 susceptible C44 pd_1 PD 21 susceptible and PD +recip.463.WT.PD3.D7 GTTTATCTTAAG 537 wild type C43 pd_1 PD 7 wild type and PD +recip.464.WT.PD3.D14 TCATCCGTCGGC 538 wild type C44 pd_1 PD 14 wild type and PD +recip.465.ASO.PD3.D14 GGCTTCGGAGCG 539 susceptible C44 pd_1 PD 14 susceptible and PD +recip.465.ASO.PD3.D7 CAGTCTAGTACG 538 wild type C44 pd_1 PD 7 wild type and PD +recip.466.ASO.PD3.D7 GTGGGACTGCGC 539 susceptible C44 pd_1 PD 7 susceptible and PD +recip.467.WT.HC3.D49.a GTCAGGTGCGGC 437 susceptible C31 hc_1 Healthy 49 susceptible and Healthy +recip.467.WT.HC3.D49.b GTTAACTTACTA 546 susceptible C49 pd_1 PD 49 susceptible and PD +recip.536.ASO.PD4.D49 CAAATTCGGGAT 547 wild type C49 pd_1 PD 49 wild type and PD +recip.537.WT.PD4.D21 CTCTATTCCACC 546 susceptible C49 pd_1 PD 21 susceptible and PD +recip.538.WT.PD4.D21 ATGGATAGCTAA 547 wild type C49 pd_1 PD 21 wild type and PD +recip.539.ASO.PD4.D14 GATCCGGCAGGA 546 susceptible C49 pd_1 PD 14 susceptible and PD +recip.539.ASO.PD4.D7 GTTCGAGTGAAT 546 susceptible C49 pd_1 PD 7 susceptible and PD +recip.540.ASO.HC4.D14 CTTCCAACTCAT 547 wild type C49 pd_1 PD 14 wild type and PD +recip.540.ASO.HC4.D7 CGGCCTAAGTTC 547 wild type C49 pd_1 PD 7 wild type and PD diff --git a/tools/suite_qiime2__stats/test-data/mann_whitney_u.test0.refdist.qza b/tools/suite_qiime2__stats/test-data/mann_whitney_u.test0.refdist.qza new file mode 100644 index 0000000..76c7834 Binary files /dev/null and b/tools/suite_qiime2__stats/test-data/mann_whitney_u.test0.refdist.qza differ diff --git a/tools/suite_qiime2__stats/test-data/mann_whitney_u.test0.timedist.qza b/tools/suite_qiime2__stats/test-data/mann_whitney_u.test0.timedist.qza new file mode 100644 index 0000000..b8e6d9e Binary files /dev/null and b/tools/suite_qiime2__stats/test-data/mann_whitney_u.test0.timedist.qza differ diff --git a/tools/suite_qiime2__stats/test-data/mann_whitney_u_facet.test0.dist.qza b/tools/suite_qiime2__stats/test-data/mann_whitney_u_facet.test0.dist.qza new file mode 100644 index 0000000..e3118c0 Binary files /dev/null and b/tools/suite_qiime2__stats/test-data/mann_whitney_u_facet.test0.dist.qza differ diff --git a/tools/suite_qiime2__stats/test-data/mann_whitney_u_facet.test1.dist.qza b/tools/suite_qiime2__stats/test-data/mann_whitney_u_facet.test1.dist.qza new file mode 100644 index 0000000..a27e8ca Binary files /dev/null and b/tools/suite_qiime2__stats/test-data/mann_whitney_u_facet.test1.dist.qza differ diff --git a/tools/suite_qiime2__stats/test-data/plot_rainclouds.test0.dist.qza b/tools/suite_qiime2__stats/test-data/plot_rainclouds.test0.dist.qza new file mode 100644 index 0000000..e96b663 Binary files /dev/null and b/tools/suite_qiime2__stats/test-data/plot_rainclouds.test0.dist.qza differ diff --git a/tools/suite_qiime2__stats/test-data/wilcoxon_srt.test0.timedist.qza b/tools/suite_qiime2__stats/test-data/wilcoxon_srt.test0.timedist.qza new file mode 100644 index 0000000..db5a390 Binary files /dev/null and b/tools/suite_qiime2__stats/test-data/wilcoxon_srt.test0.timedist.qza differ diff --git a/tools/suite_qiime2__stats/test-data/wilcoxon_srt_facet.test0.dist.qza b/tools/suite_qiime2__stats/test-data/wilcoxon_srt_facet.test0.dist.qza new file mode 100644 index 0000000..256c550 Binary files /dev/null and b/tools/suite_qiime2__stats/test-data/wilcoxon_srt_facet.test0.dist.qza differ diff --git a/tools/suite_qiime2__taxa/qiime2__taxa__barplot.xml b/tools/suite_qiime2__taxa/qiime2__taxa__barplot.xml index 941a637..5b01ff7 100644 --- a/tools/suite_qiime2__taxa/qiime2__taxa__barplot.xml +++ b/tools/suite_qiime2__taxa/qiime2__taxa__barplot.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Visualize taxonomy with an interactive bar plot + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version taxa q2galaxy run taxa barplot '$inputs' diff --git a/tools/suite_qiime2__taxa/qiime2__taxa__collapse.xml b/tools/suite_qiime2__taxa/qiime2__taxa__collapse.xml index 62f71fe..689e4fc 100644 --- a/tools/suite_qiime2__taxa/qiime2__taxa__collapse.xml +++ b/tools/suite_qiime2__taxa/qiime2__taxa__collapse.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Collapse features by their taxonomy at the specified level + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version taxa q2galaxy run taxa collapse '$inputs' diff --git a/tools/suite_qiime2__taxa/qiime2__taxa__filter_seqs.xml b/tools/suite_qiime2__taxa/qiime2__taxa__filter_seqs.xml index 7818d9f..efaa622 100644 --- a/tools/suite_qiime2__taxa/qiime2__taxa__filter_seqs.xml +++ b/tools/suite_qiime2__taxa/qiime2__taxa__filter_seqs.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Taxonomy-based feature sequence filter. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version taxa q2galaxy run taxa filter_seqs '$inputs' diff --git a/tools/suite_qiime2__taxa/qiime2__taxa__filter_table.xml b/tools/suite_qiime2__taxa/qiime2__taxa__filter_table.xml index 9254889..9793b3c 100644 --- a/tools/suite_qiime2__taxa/qiime2__taxa__filter_table.xml +++ b/tools/suite_qiime2__taxa/qiime2__taxa__filter_table.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Taxonomy-based feature table filter. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version taxa q2galaxy run taxa filter_table '$inputs' diff --git a/tools/suite_qiime2__taxa/test-data/barplot.test0.table.qza b/tools/suite_qiime2__taxa/test-data/barplot.test0.table.qza index 5d9adc8..2621ec5 100644 Binary files a/tools/suite_qiime2__taxa/test-data/barplot.test0.table.qza and b/tools/suite_qiime2__taxa/test-data/barplot.test0.table.qza differ diff --git a/tools/suite_qiime2__taxa/test-data/barplot.test0.taxonomy.qza b/tools/suite_qiime2__taxa/test-data/barplot.test0.taxonomy.qza index d42f047..979c697 100644 Binary files a/tools/suite_qiime2__taxa/test-data/barplot.test0.taxonomy.qza and b/tools/suite_qiime2__taxa/test-data/barplot.test0.taxonomy.qza differ diff --git a/tools/suite_qiime2__taxa/test-data/collapse.test0.table.qza b/tools/suite_qiime2__taxa/test-data/collapse.test0.table.qza index 5d9adc8..2621ec5 100644 Binary files a/tools/suite_qiime2__taxa/test-data/collapse.test0.table.qza and b/tools/suite_qiime2__taxa/test-data/collapse.test0.table.qza differ diff --git a/tools/suite_qiime2__taxa/test-data/collapse.test0.taxonomy.qza b/tools/suite_qiime2__taxa/test-data/collapse.test0.taxonomy.qza index d42f047..979c697 100644 Binary files a/tools/suite_qiime2__taxa/test-data/collapse.test0.taxonomy.qza and b/tools/suite_qiime2__taxa/test-data/collapse.test0.taxonomy.qza differ diff --git a/tools/suite_qiime2__vizard/.shed.yml b/tools/suite_qiime2__vizard/.shed.yml new file mode 100644 index 0000000..5ea014b --- /dev/null +++ b/tools/suite_qiime2__vizard/.shed.yml @@ -0,0 +1,17 @@ +owner: q2d2 +type: unrestricted +homepage_url: https://github.com/qiime2/q2-vizard +remote_repository_url: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard +categories: + - Metagenomics + - Sequence Analysis + - Statistics +auto_tool_repositories: + name_template: '{{ tool_id }}' + description_template: 'Galaxy tool for QIIME 2 action: ''{{tool_name}}''.' +suite: + name: suite_qiime2__vizard + description: 'Galaxy suite for QIIME 2 plugin: ''vizard''. Generalized microbiome + data visualization.' + long_description: This QIIME 2 plugin is the first choice of wizard lizards for + generalized microbiome data visualization! diff --git a/tools/suite_qiime2__vizard/qiime2__vizard__boxplot.xml b/tools/suite_qiime2__vizard/qiime2__vizard__boxplot.xml new file mode 100644 index 0000000..1d56648 --- /dev/null +++ b/tools/suite_qiime2__vizard/qiime2__vizard__boxplot.xml @@ -0,0 +1,118 @@ + + + + + Boxplot + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version vizard + q2galaxy run vizard boxplot '$inputs' + + + + + + + + + + + + + + + + + + + + + + + value is not None and len(value) > 0 + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + +QIIME 2: vizard boxplot +======================= +Boxplot + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Basic boxplot for visualizing a numeric Metadata measure grouped by a categorical Metadata measure with choices for the whisker range. + + +| + + + + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__vizard/qiime2__vizard__heatmap.xml b/tools/suite_qiime2__vizard/qiime2__vizard__heatmap.xml new file mode 100644 index 0000000..c45279a --- /dev/null +++ b/tools/suite_qiime2__vizard/qiime2__vizard__heatmap.xml @@ -0,0 +1,149 @@ + + + + + Heatmap + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version vizard + q2galaxy run vizard heatmap '$inputs' + + + + + + + + + + + + + + + + + + + + + + + value is not None and len(value) > 0 + + + + + + value is not None and len(value) > 0 + + + + + + value is not None and len(value) > 0 + +
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +QIIME 2: vizard heatmap +======================= +Heatmap + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Basic heatmap for visualizing three Metadata measures. + +Examples: +--------- + +heatmap +******* +Using the ``qiime2 vizard heatmap`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Set *"gradient_measure"* to ``a`` + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 vizard heatmap [...] : visualization.qzv`` + - ``heatmap.qzv`` + + +| + + + + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__vizard/qiime2__vizard__lineplot.xml b/tools/suite_qiime2__vizard/qiime2__vizard__lineplot.xml new file mode 100644 index 0000000..aed40ed --- /dev/null +++ b/tools/suite_qiime2__vizard/qiime2__vizard__lineplot.xml @@ -0,0 +1,396 @@ + + + + + Lineplot + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version vizard + q2galaxy run vizard lineplot '$inputs' + + + + + + + + + + + + + + + + + + + + + + + value is not None and len(value) > 0 + + + + + + value is not None and len(value) > 0 + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +QIIME 2: vizard lineplot +======================== +Lineplot + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Basic lineplot for visualizing two numeric Metadata measures with optional grouping. All numeric columns present in the Metadata will be available as drop-down options on the Y-axis, but the chosen `x_measure` remains fixed. + +Examples: +--------- + +lineplot_median_replicates_with_grouping +**************************************** +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"replicate_method"* to ``median`` + #. Set *"group_by"* to ``group`` + #. Set *"title"* to ``Lineplot with median replicate method, grouped by `group`.`` + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_mean_replicates_with_grouping +************************************** +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"replicate_method"* to ``mean`` + #. Set *"group_by"* to ``group`` + #. Set *"title"* to ``Lineplot with mean replicate method, grouped by `group`.`` + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_median_replicates_no_grouping +************************************** +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"replicate_method"* to ``median`` + #. Set *"title"* to ``Lineplot with median replicate method (no grouping).`` + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_mean_replicates_no_grouping +************************************ +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"replicate_method"* to ``mean`` + #. Set *"title"* to ``Lineplot with mean replicate method (no grouping).`` + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_no_replicates_with_grouping +************************************ +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``a`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"group_by"* to ``group`` + #. Set *"title"* to ``Lineplot with no replicate method, grouped by `group`.`` + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_no_replicates_no_grouping +********************************** +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``b`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + - Set *"title"* to ``Lineplot with no replicate method (no grouping).`` + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + + +| + + + + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__vizard/qiime2__vizard__scatterplot_2d.xml b/tools/suite_qiime2__vizard/qiime2__vizard__scatterplot_2d.xml new file mode 100644 index 0000000..e080b6f --- /dev/null +++ b/tools/suite_qiime2__vizard/qiime2__vizard__scatterplot_2d.xml @@ -0,0 +1,216 @@ + + + + + 2D Scatterplot + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version vizard + q2galaxy run vizard scatterplot_2d '$inputs' + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +QIIME 2: vizard scatterplot-2d +============================== +2D Scatterplot + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping. + +Examples: +--------- + +scatterplot_defaults +******************** +Using the ``qiime2 vizard scatterplot-2d`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 vizard scatterplot-2d [...] : visualization.qzv`` + - ``scatterplot.qzv`` + +scatterplot_all_measures +************************ +Using the ``qiime2 vizard scatterplot-2d`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Expand the ``additional options`` section + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Set *"color_by"* to ``group`` + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 vizard scatterplot-2d [...] : visualization.qzv`` + - ``scatterplot.qzv`` + + +| + + + + 10.1038/s41587-019-0209-9 + + diff --git a/tools/suite_qiime2__vizard/test-data/heatmap.test0.metadata.tsv b/tools/suite_qiime2__vizard/test-data/heatmap.test0.metadata.tsv new file mode 100644 index 0000000..3ef7b52 --- /dev/null +++ b/tools/suite_qiime2__vizard/test-data/heatmap.test0.metadata.tsv @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff --git a/tools/suite_qiime2__vizard/test-data/lineplot.test0.metadata.tsv b/tools/suite_qiime2__vizard/test-data/lineplot.test0.metadata.tsv new file mode 100644 index 0000000..3ef7b52 --- /dev/null +++ b/tools/suite_qiime2__vizard/test-data/lineplot.test0.metadata.tsv @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff --git a/tools/suite_qiime2__vizard/test-data/lineplot.test1.metadata.tsv b/tools/suite_qiime2__vizard/test-data/lineplot.test1.metadata.tsv new file mode 100644 index 0000000..3ef7b52 --- /dev/null +++ b/tools/suite_qiime2__vizard/test-data/lineplot.test1.metadata.tsv @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff --git a/tools/suite_qiime2__vizard/test-data/lineplot.test2.metadata.tsv b/tools/suite_qiime2__vizard/test-data/lineplot.test2.metadata.tsv new file mode 100644 index 0000000..3ef7b52 --- /dev/null +++ b/tools/suite_qiime2__vizard/test-data/lineplot.test2.metadata.tsv @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff --git a/tools/suite_qiime2__vizard/test-data/lineplot.test3.metadata.tsv b/tools/suite_qiime2__vizard/test-data/lineplot.test3.metadata.tsv new file mode 100644 index 0000000..3ef7b52 --- /dev/null +++ b/tools/suite_qiime2__vizard/test-data/lineplot.test3.metadata.tsv @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff --git a/tools/suite_qiime2__vizard/test-data/lineplot.test4.metadata.tsv b/tools/suite_qiime2__vizard/test-data/lineplot.test4.metadata.tsv new file mode 100644 index 0000000..3ef7b52 --- /dev/null +++ b/tools/suite_qiime2__vizard/test-data/lineplot.test4.metadata.tsv @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff --git a/tools/suite_qiime2__vizard/test-data/lineplot.test5.metadata.tsv b/tools/suite_qiime2__vizard/test-data/lineplot.test5.metadata.tsv new file mode 100644 index 0000000..3ef7b52 --- /dev/null +++ b/tools/suite_qiime2__vizard/test-data/lineplot.test5.metadata.tsv @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff --git a/tools/suite_qiime2__vizard/test-data/scatterplot_2d.test0.metadata.tsv b/tools/suite_qiime2__vizard/test-data/scatterplot_2d.test0.metadata.tsv new file mode 100644 index 0000000..3ef7b52 --- /dev/null +++ b/tools/suite_qiime2__vizard/test-data/scatterplot_2d.test0.metadata.tsv @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff --git a/tools/suite_qiime2__vizard/test-data/scatterplot_2d.test1.metadata.tsv b/tools/suite_qiime2__vizard/test-data/scatterplot_2d.test1.metadata.tsv new file mode 100644 index 0000000..3ef7b52 --- /dev/null +++ b/tools/suite_qiime2__vizard/test-data/scatterplot_2d.test1.metadata.tsv @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_closed_reference.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_closed_reference.xml index b2d5895..d4c8e7b 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_closed_reference.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_closed_reference.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Closed-reference clustering of features. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version vsearch q2galaxy run vsearch cluster_features_closed_reference '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_de_novo.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_de_novo.xml index 94a8c55..d2a272e 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_de_novo.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_de_novo.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + De novo clustering of features. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version vsearch q2galaxy run vsearch cluster_features_de_novo '$inputs' @@ -45,7 +48,28 @@ for: - + + + + + + + + + + + + + + + + + + + + + + QIIME 2: vsearch cluster-features-de-novo ========================================= @@ -63,6 +87,22 @@ Description: ------------ Given a feature table and the associated feature sequences, cluster the features based on user-specified percent identity threshold of their sequences. This is not a general-purpose de novo clustering method, but rather is intended to be used for clustering the results of quality-filtering/dereplication methods, such as DADA2, or for re-clustering a FeatureTable at a lower percent identity than it was originally clustered at. When a group of features in the input table are clustered into a single feature, the frequency of that single feature in a given sample is the sum of the frequencies of the features that were clustered in that sample. Feature identifiers and sequences will be inherited from the centroid feature of each cluster. See the vsearch documentation for details on how sequence clustering is performed. +Examples: +--------- + +cluster_features_de_novo +************************ +Using the ``qiime2 vsearch cluster-features-de-novo`` tool: + #. Set *"sequences"* to ``#: seqs1.qza`` + #. Set *"table"* to ``#: table1.qza`` + #. Set *"perc_identity"* to ``0.97`` + #. Expand the ``additional options`` section + + - Leave *"strand"* as its default value of ``plus`` + + #. Press the ``Execute`` button. + + | diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_open_reference.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_open_reference.xml index 49b47af..c73b2c2 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_open_reference.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_open_reference.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Open-reference clustering of features. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version vsearch q2galaxy run vsearch cluster_features_open_reference '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__dereplicate_sequences.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__dereplicate_sequences.xml index a655d19..5b0e847 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__dereplicate_sequences.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__dereplicate_sequences.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Dereplicate sequences. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version vsearch q2galaxy run vsearch dereplicate_sequences '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__fastq_stats.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__fastq_stats.xml index 703614b..b2fb127 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__fastq_stats.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__fastq_stats.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Fastq stats with vsearch. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version vsearch q2galaxy run vsearch fastq_stats '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__merge_pairs.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__merge_pairs.xml index 9aa92e9..8199b32 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__merge_pairs.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__merge_pairs.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Merge paired-end reads. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version vsearch q2galaxy run vsearch merge_pairs '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_denovo.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_denovo.xml index 09dfff3..34b886a 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_denovo.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_denovo.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + De novo chimera filtering with vsearch. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version vsearch q2galaxy run vsearch uchime_denovo '$inputs' diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_ref.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_ref.xml index 623842b..469b232 100644 --- a/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_ref.xml +++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_ref.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Reference-based chimera filtering with vsearch. + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy version vsearch q2galaxy run vsearch uchime_ref '$inputs' diff --git a/tools/suite_qiime2__vsearch/test-data/.gitkeep b/tools/suite_qiime2__vsearch/test-data/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/tools/suite_qiime2__vsearch/test-data/cluster_features_de_novo.test0.seqs1.qza b/tools/suite_qiime2__vsearch/test-data/cluster_features_de_novo.test0.seqs1.qza new file mode 100644 index 0000000..4d216f1 Binary files /dev/null and b/tools/suite_qiime2__vsearch/test-data/cluster_features_de_novo.test0.seqs1.qza differ diff --git a/tools/suite_qiime2__vsearch/test-data/cluster_features_de_novo.test0.table1.qza b/tools/suite_qiime2__vsearch/test-data/cluster_features_de_novo.test0.table1.qza new file mode 100644 index 0000000..6077c78 Binary files /dev/null and b/tools/suite_qiime2__vsearch/test-data/cluster_features_de_novo.test0.table1.qza differ diff --git a/tools/suite_qiime2_core__tools/qiime2_core__tools__export.xml b/tools/suite_qiime2_core__tools/qiime2_core__tools__export.xml index c4d000b..ef7fa04 100644 --- a/tools/suite_qiime2_core__tools/qiime2_core__tools__export.xml +++ b/tools/suite_qiime2_core__tools/qiime2_core__tools__export.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Export data from a QIIME 2 artifact + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy run tools export '$inputs' @@ -38,6 +41,16 @@ for: + + + + + + + + + + @@ -52,12 +65,9 @@ for: - - - @@ -73,12 +83,15 @@ for: + - + + + @@ -92,6 +105,15 @@ for: + + + + + + + + + @@ -101,7 +123,6 @@ for: - @@ -113,6 +134,8 @@ for: + + @@ -123,6 +146,7 @@ for: + @@ -155,6 +179,66 @@ for: + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -239,12 +323,6 @@ for: - - - - - - @@ -263,18 +341,6 @@ for: - - - - - - - - - - - - @@ -374,6 +440,14 @@ for: + + + + + + + + @@ -398,10 +472,10 @@ for: - + - + @@ -416,6 +490,18 @@ for: + + + + + + + + + + + + @@ -449,6 +535,7 @@ for: + @@ -493,6 +580,60 @@ for: + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -547,12 +688,6 @@ for: - - - - - - @@ -622,6 +757,18 @@ for: + + + + + + + + + + + + @@ -686,6 +833,12 @@ for: + + + + + + @@ -702,7 +855,7 @@ for: - fmt_finder['output_format'] == 'None' and fmt_peek not in {'PredictionsDirectoryFormat', 'QualityFilterStatsDirFmt', 'ProteinSequencesDirectoryFormat', 'OrthologAnnotationDirFmt', 'FirstDifferencesDirectoryFormat', 'DecontamScoreDirFmt', 'BooleanSeriesFormat', 'Bowtie2IndexDirFmt', 'GenesDirectoryFormat', 'AlphaDiversityFormat', 'SILVATaxidMapFormat', 'RNASequencesDirectoryFormat', 'MultiBAMDirFmt', 'AlignedDNAFASTAFormat', 'SILVATaxonomyDirectoryFormat', 'SeedOrthologDirFmt', 'QIIME1DemuxDirFmt', 'ImportanceDirectoryFormat', 'BooleanSeriesDirectoryFormat', 'BLAST6DirectoryFormat', 'BAMDirFmt', 'ImmutableMetadataFormat', 'QualityFilterStatsFmt', 'Kraken2DBReportDirectoryFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'MAGtoContigsDirFmt', 'AlignedRNASequencesDirectoryFormat', 'NewickFormat', 'NewickDirectoryFormat', 'ProcrustesStatisticsFmt', 'EMPSingleEndDirFmt', 'PlacementsFormat', 'LSMatFormat', 'OrdinationFormat', 'AlignedProteinFASTAFormat', 'DifferentialFormat', 'SILVATaxidMapDirectoryFormat', 'CasavaOneEightSingleLanePerSampleDirFmt', 'ProbabilitiesFormat', 'DADA2StatsFormat', 'DNASequencesDirectoryFormat', 'EMPPairedEndDirFmt', 'SequenceCharacteristicsFormat', 'DiamondDatabaseFileFmt', 'ImmutableMetadataDirectoryFormat', 'OrdinationDirectoryFormat', 'MultiBowtie2IndexDirFmt', 'SILVATaxonomyFormat', 'DistanceMatrixDirectoryFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'DiamondDatabaseDirFmt', 'BIOMV210DirFmt', 'BIOMV210Format', 'LociDirectoryFormat', 'QIIME1DemuxFormat', 'Kraken2ReportDirectoryFormat', 'TSVTaxonomyFormat', 'KaijuDBDirectoryFormat', 'ErrorCorrectionDetailsFmt', 'NCBITaxonomyDirFmt', 'AlignedProteinSequencesDirectoryFormat', 'ProteinFASTAFormat', 'AlphaDiversityDirectoryFormat', 'FastqGzFormat', 'ImportanceFormat', 'ContigSequencesDirFmt', 'RNAFASTAFormat', 'ErrorCorrectionDetailsDirFmt', 'SequenceCharacteristicsDirectoryFormat', 'UchimeStatsDirFmt', 'MAGSequencesDirFmt', 'PairedRNASequencesDirectoryFormat', 'DNAFASTAFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'DataLoafPackageDirFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'MultiFASTADirectoryFormat', 'BLASTDBDirFmtV5', 'BrackenDBDirectoryFormat', 'FirstDifferencesFormat', 'TSVTaxonomyDirectoryFormat', 'DifferentialDirectoryFormat', 'MultiMAGSequencesDirFmt', 'PlacementsDirFmt', 'BLAST6Format', 'AlignedRNAFASTAFormat', 'TrueTargetsDirectoryFormat', 'ArtificialGroupingDirectoryFormat', 'ProcrustesStatisticsDirFmt', 'ProteinsDirectoryFormat', 'MAGtoContigsFormat', 'AlignedDNASequencesDirectoryFormat', 'ArtificialGroupingFormat', 'SeppReferenceDirFmt', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'EggnogProteinSequencesDirFmt', 'ProbabilitiesDirectoryFormat', 'DeblurStatsDirFmt', 'DADA2StatsDirFmt', 'DecontamScoreFormat', 'UchimeStatsFmt', 'SampleEstimatorDirFmt', 'EggnogRefDirFmt', 'DeblurStatsFmt', 'PairedDNASequencesDirectoryFormat', 'Kraken2OutputDirectoryFormat', 'PredictionsFormat', 'Kraken2DBDirectoryFormat'} + fmt_finder['output_format'] == 'None' and fmt_peek not in {'QIIME1DemuxFormat', 'TSVTaxonomyFormat', 'ProcrustesStatisticsDirFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'UchimeStatsDirFmt', 'SILVATaxidMapFormat', 'NewickDirectoryFormat', 'AlignedDNAFASTAFormat', 'OrdinationDirectoryFormat', 'TableJSONLFileFormat', 'ProteinsDirectoryFormat', 'AlignedProteinSequencesDirectoryFormat', 'ArtificialGroupingDirectoryFormat', 'QualityFilterStatsFmt', 'ImmutableMetadataDirectoryFormat', 'DistanceMatrixDirectoryFormat', 'UchimeStatsFmt', 'ProteinSingleProfileHmmDirectoryFmt', 'DADA2StatsFormat', 'BIOMV210DirFmt', 'MultiFASTADirectoryFormat', 'AlignedDNASequencesDirectoryFormat', 'TableJSONLDirFmt', 'SequenceCharacteristicsFormat', 'BooleanSeriesFormat', 'MultiBAMDirFmt', 'GenomeSequencesDirectoryFormat', 'AlignedRNASequencesDirectoryFormat', 'MultiBowtie2IndexDirFmt', 'ImportanceFormat', 'FirstDifferencesDirectoryFormat', 'ArtificialGroupingFormat', 'MAGtoContigsFormat', 'MAGSequencesDirFmt', 'KaijuDBDirectoryFormat', 'DiamondDatabaseFileFmt', 'DataLoafPackageDirFmt', 'QIIME1DemuxDirFmt', 'DNASingleProfileHmmDirectoryFmt', 'Kraken2ReportDirectoryFormat', 'ErrorCorrectionDetailsDirFmt', 'ProbabilitiesDirectoryFormat', 'DecontamScoreDirFmt', 'DeblurStatsDirFmt', 'SILVATaxidMapDirectoryFormat', 'SingleLanePerSampleSingleEndFastqDirFmt', 'BLASTDBDirFmtV5', 'ErrorCorrectionDetailsFmt', 'LociDirectoryFormat', 'FastqGzFormat', 'ImmutableMetadataFormat', 'RNAFASTAFormat', 'EggnogRefDirFmt', 'DNAFASTAFormat', 'PlacementsDirFmt', 'ProteinMultipleProfileHmmDirectoryFmt', 'EMPSingleEndDirFmt', 'SILVATaxonomyDirectoryFormat', 'BLAST6Format', 'DNAMultipleProfileHmmDirectoryFmt', 'DADA2StatsDirFmt', 'SILVATaxonomyFormat', 'DNASequencesDirectoryFormat', 'PairedRNASequencesDirectoryFormat', 'SeedOrthologDirFmt', 'SequenceCharacteristicsDirectoryFormat', 'ProbabilitiesFormat', 'Kraken2DBReportDirectoryFormat', 'QualityFilterStatsDirFmt', 'SingleLanePerSamplePairedEndFastqDirFmt', 'DifferentialFormat', 'BAMDirFmt', 'NCBITaxonomyDirFmt', 'NewickFormat', 'LSMatFormat', 'MultiMAGSequencesDirFmt', 'RNASingleProfileHmmDirectoryFmt', 'Kraken2DBDirectoryFormat', 'AlignedRNAFASTAFormat', 'ProteinSequencesDirectoryFormat', 'Kraken2OutputDirectoryFormat', 'SampleEstimatorDirFmt', 'RNAMultipleProfileHmmDirectoryFmt', 'ProcrustesStatisticsFmt', 'BooleanSeriesDirectoryFormat', 'FirstDifferencesFormat', 'Bowtie2IndexDirFmt', 'PredictionsFormat', 'BLAST6DirectoryFormat', 'ImportanceDirectoryFormat', 'DifferentialDirectoryFormat', 'EMPPairedEndDirFmt', 'SeppReferenceDirFmt', 'TrueTargetsDirectoryFormat', 'OrdinationFormat', 'EggnogProteinSequencesDirFmt', 'OrthologAnnotationDirFmt', 'DecontamScoreFormat', 'DeblurStatsFmt', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'MAGtoContigsDirFmt', 'Kraken2DBReportFormat', 'GenesDirectoryFormat', 'PredictionsDirectoryFormat', 'DiamondDatabaseDirFmt', 'TSVTaxonomyDirectoryFormat', 'ProteinFASTAFormat', 'BIOMV210Format', 'PairedDNASequencesDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'AlphaDiversityDirectoryFormat', 'RNASequencesDirectoryFormat', 'AlignedProteinFASTAFormat', 'PlacementsFormat', 'AlphaDiversityFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'ContigSequencesDirFmt', 'PressedProfileHmmsDirectoryFmt', 'BrackenDBDirectoryFormat'} @@ -817,10 +970,18 @@ for: fmt_finder['output_format'] == 'DNAFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNAFASTAFormat') + + fmt_finder['output_format'] == 'DNAMultipleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNAMultipleProfileHmmDirectoryFmt') + + fmt_finder['output_format'] == 'DNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNASequencesDirectoryFormat') + + fmt_finder['output_format'] == 'DNASingleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DNASingleProfileHmmDirectoryFmt') + + fmt_finder['output_format'] == 'DataLoafPackageDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'DataLoafPackageDirFmt') @@ -909,6 +1070,10 @@ for: fmt_finder['output_format'] == 'GenesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'GenesDirectoryFormat') + + fmt_finder['output_format'] == 'GenomeSequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'GenomeSequencesDirectoryFormat') + + fmt_finder['output_format'] == 'ImmutableMetadataDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ImmutableMetadataDirectoryFormat') @@ -941,6 +1106,10 @@ for: fmt_finder['output_format'] == 'Kraken2DBReportDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBReportDirectoryFormat') + + fmt_finder['output_format'] == 'Kraken2DBReportFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2DBReportFormat') + + fmt_finder['output_format'] == 'Kraken2OutputDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'Kraken2OutputDirectoryFormat') @@ -1055,6 +1224,13 @@ for: fmt_finder['output_format'] == 'PredictionsFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PredictionsFormat') + + fmt_finder['output_format'] == 'PressedProfileHmmsDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'PressedProfileHmmsDirectoryFmt') + + + + + fmt_finder['output_format'] == 'ProbabilitiesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProbabilitiesDirectoryFormat') @@ -1075,10 +1251,18 @@ for: fmt_finder['output_format'] == 'ProteinFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinFASTAFormat') + + fmt_finder['output_format'] == 'ProteinMultipleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinMultipleProfileHmmDirectoryFmt') + + fmt_finder['output_format'] == 'ProteinSequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinSequencesDirectoryFormat') + + fmt_finder['output_format'] == 'ProteinSingleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinSingleProfileHmmDirectoryFmt') + + fmt_finder['output_format'] == 'ProteinsDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'ProteinsDirectoryFormat') @@ -1103,10 +1287,18 @@ for: fmt_finder['output_format'] == 'RNAFASTAFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNAFASTAFormat') + + fmt_finder['output_format'] == 'RNAMultipleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNAMultipleProfileHmmDirectoryFmt') + + fmt_finder['output_format'] == 'RNASequencesDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNASequencesDirectoryFormat') + + fmt_finder['output_format'] == 'RNASingleProfileHmmDirectoryFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'RNASingleProfileHmmDirectoryFmt') + + fmt_finder['output_format'] == 'SILVATaxidMapDirectoryFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'SILVATaxidMapDirectoryFormat') @@ -1172,6 +1364,14 @@ for: fmt_finder['output_format'] == 'TSVTaxonomyFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TSVTaxonomyFormat') + + fmt_finder['output_format'] == 'TableJSONLDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TableJSONLDirFmt') + + + + fmt_finder['output_format'] == 'TableJSONLFileFormat' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TableJSONLFileFormat') + + fmt_finder['output_format'] == 'TaxonomicClassiferTemporaryPickleDirFmt' or (fmt_finder['output_format'] == 'None' and fmt_peek == 'TaxonomicClassiferTemporaryPickleDirFmt') @@ -1214,10 +1414,29 @@ Formats: -------- These formats have documentation available. -FastqGzFormat -************* +PressedProfileHmmsDirectoryFmt +****************************** -A gzipped fastq file. +The <hmmfile>.h3m file contains the profile HMMs +and their annotation in a binary format. The <hmmfile>.h3i file is an +SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains +precomputed data structures for the fast heuristic filter +(the MSV filter). The <hmmfile>.h3p file contains precomputed data +structures for the rest of each profile. + +TSVTaxonomyFormat +***************** +Format for a 2+ column TSV file with an expected minimal header. + +The only header recognized by this format is: + + Feature ID<tab>Taxon + +Optionally followed by other arbitrary columns. + +This format supports blank lines. The expected header must be the first +non-blank line. In addition to the header, there must be at least one line +of data. QIIME1DemuxFormat @@ -1268,127 +1487,128 @@ tied to a property. For example the "validate_seq_char_len" validator for "FeatureData[SequenceCharacteristics % Properties("length")]" adds validation for a numerical column called "length". -TSVTaxonomyFormat -***************** -Format for a 2+ column TSV file with an expected minimal header. - -The only header recognized by this format is: - - Feature ID<tab>Taxon - -Optionally followed by other arbitrary columns. +FastqGzFormat +************* -This format supports blank lines. The expected header must be the first -non-blank line. In addition to the header, there must be at least one line -of data. +A gzipped fastq file. Additional formats without documentation: ***************************************** - - DataLoafPackageDirFmt - - EggnogRefDirFmt - - NCBITaxonomyDirFmt - - BIOMV210DirFmt - - FirstDifferencesDirectoryFormat - - PredictionsDirectoryFormat - - QIIME1DemuxDirFmt - - SILVATaxonomyFormat - - MAGSequencesDirFmt - - AlphaDiversityDirectoryFormat - - Kraken2OutputDirectoryFormat - - BAMDirFmt - - TSVTaxonomyDirectoryFormat - - EggnogProteinSequencesDirFmt - - ImmutableMetadataFormat - - LSMatFormat - - SingleLanePerSampleSingleEndFastqDirFmt - - AlignedProteinFASTAFormat - - PairedDNASequencesDirectoryFormat - - BooleanSeriesFormat - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - DecontamScoreFormat - - OrthologAnnotationDirFmt - - GenesDirectoryFormat - - MultiBAMDirFmt - - BIOMV210Format - - DecontamScoreDirFmt - - ErrorCorrectionDetailsFmt - - DiamondDatabaseFileFmt - - AlignedProteinSequencesDirectoryFormat - - PairedRNASequencesDirectoryFormat - DifferentialFormat - - Kraken2DBDirectoryFormat - - DADA2StatsFormat - DNASequencesDirectoryFormat - - ErrorCorrectionDetailsDirFmt - - DiamondDatabaseDirFmt - - ImmutableMetadataDirectoryFormat - - BooleanSeriesDirectoryFormat + - Kraken2OutputDirectoryFormat + - MultiBAMDirFmt + - FirstDifferencesFormat - AlignedDNAFASTAFormat + - ProcrustesStatisticsDirFmt + - EggnogProteinSequencesDirFmt + - DifferentialDirectoryFormat + - MAGSequencesDirFmt + - ProteinSingleProfileHmmDirectoryFmt - ImportanceFormat - - NewickFormat - - DistanceMatrixDirectoryFormat - - SingleLanePerSamplePairedEndFastqDirFmt - - PlacementsDirFmt - - DeblurStatsFmt - - SILVATaxidMapDirectoryFormat - - QualityFilterStatsFmt + - ImmutableMetadataFormat + - ErrorCorrectionDetailsFmt + - ArtificialGroupingFormat + - OrthologAnnotationDirFmt + - DecontamScoreFormat + - FirstDifferencesDirectoryFormat + - TrueTargetsDirectoryFormat - AlignedDNASequencesDirectoryFormat + - QualityFilterStatsFmt + - DeblurStatsFmt + - BooleanSeriesDirectoryFormat + - BIOMV210DirFmt + - OrdinationFormat + - LSMatFormat + - ProteinMultipleProfileHmmDirectoryFmt - ImportanceDirectoryFormat - - NewickDirectoryFormat - - MultiplexedSingleEndBarcodeInSequenceDirFmt - - MultiFASTADirectoryFormat - - ProcrustesStatisticsFmt - - SILVATaxidMapFormat - - UchimeStatsDirFmt - - Kraken2ReportDirectoryFormat + - ImmutableMetadataDirectoryFormat + - ErrorCorrectionDetailsDirFmt + - SingleLanePerSamplePairedEndFastqDirFmt + - Kraken2DBDirectoryFormat + - OrdinationDirectoryFormat + - BooleanSeriesFormat + - BLASTDBDirFmtV5 + - DADA2StatsFormat - BLAST6Format - - QualityFilterStatsDirFmt - - ProbabilitiesFormat - - SILVATaxonomyDirectoryFormat - - MultiMAGSequencesDirFmt - - EMPSingleEndDirFmt - - Bowtie2IndexDirFmt - - ProcrustesStatisticsDirFmt - - DeblurStatsDirFmt + - KaijuDBDirectoryFormat - ArtificialGroupingDirectoryFormat - - TaxonomicClassiferTemporaryPickleDirFmt - - LociDirectoryFormat - - ArtificialGroupingFormat + - MultiFASTADirectoryFormat - MAGtoContigsFormat - - BrackenDBDirectoryFormat - - ProteinFASTAFormat + - DNASingleProfileHmmDirectoryFmt - RNAFASTAFormat - - DADA2StatsDirFmt + - ProbabilitiesFormat + - SampleEstimatorDirFmt + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - TableJSONLFileFormat + - LociDirectoryFormat + - QualityFilterStatsDirFmt + - TSVTaxonomyDirectoryFormat + - UchimeStatsFmt + - ProcrustesStatisticsFmt + - SILVATaxonomyDirectoryFormat + - AlphaDiversityFormat - BLAST6DirectoryFormat + - MultiMAGSequencesDirFmt + - SeppReferenceDirFmt + - DNAMultipleProfileHmmDirectoryFmt + - RNASequencesDirectoryFormat - ProbabilitiesDirectoryFormat - - MultiBowtie2IndexDirFmt - - EMPPairedEndDirFmt - - OrdinationFormat - - SeedOrthologDirFmt - - MAGtoContigsDirFmt - - SampleEstimatorDirFmt + - PredictionsFormat - PlacementsFormat + - NewickFormat + - TableJSONLDirFmt + - BrackenDBDirectoryFormat - ProteinSequencesDirectoryFormat - - RNASequencesDirectoryFormat - - DNAFASTAFormat - - UchimeStatsFmt + - GenomeSequencesDirectoryFormat + - MultiplexedSingleEndBarcodeInSequenceDirFmt + - EggnogRefDirFmt + - UchimeStatsDirFmt - AlignedRNAFASTAFormat - - TrueTargetsDirectoryFormat - - Kraken2DBReportDirectoryFormat - - KaijuDBDirectoryFormat - - ContigSequencesDirFmt - - FirstDifferencesFormat - - SeppReferenceDirFmt - - OrdinationDirectoryFormat - - PredictionsFormat - - ProteinsDirectoryFormat - - BLASTDBDirFmtV5 + - EMPSingleEndDirFmt + - DADA2StatsDirFmt + - TaxonomicClassiferTemporaryPickleDirFmt + - AlphaDiversityDirectoryFormat + - Kraken2ReportDirectoryFormat + - MultiBowtie2IndexDirFmt + - SILVATaxidMapFormat + - CasavaOneEightSingleLanePerSampleDirFmt + - RNASingleProfileHmmDirectoryFmt + - PredictionsDirectoryFormat + - DeblurStatsDirFmt + - Bowtie2IndexDirFmt + - SeedOrthologDirFmt + - DiamondDatabaseFileFmt + - ProteinFASTAFormat - AlignedRNASequencesDirectoryFormat + - EMPPairedEndDirFmt + - NewickDirectoryFormat - SequenceCharacteristicsDirectoryFormat - - AlphaDiversityFormat - - CasavaOneEightSingleLanePerSampleDirFmt - - DifferentialDirectoryFormat + - ContigSequencesDirFmt + - Kraken2DBReportFormat + - RNAMultipleProfileHmmDirectoryFmt + - PlacementsDirFmt + - DecontamScoreDirFmt + - SILVATaxonomyFormat + - DataLoafPackageDirFmt + - SILVATaxidMapDirectoryFormat + - DNAFASTAFormat + - ProteinsDirectoryFormat + - MAGtoContigsDirFmt + - QIIME1DemuxDirFmt + - DiamondDatabaseDirFmt + - Kraken2DBReportDirectoryFormat + - PairedDNASequencesDirectoryFormat + - NCBITaxonomyDirFmt + - DistanceMatrixDirectoryFormat + - BIOMV210Format + - AlignedProteinFASTAFormat + - SingleLanePerSampleSingleEndFastqDirFmt + - BAMDirFmt + - PairedRNASequencesDirectoryFormat + - AlignedProteinSequencesDirectoryFormat + - GenesDirectoryFormat 10.1038/s41587-019-0209-9 diff --git a/tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml b/tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml index bf27578..945905d 100644 --- a/tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml +++ b/tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Import data into a QIIME 2 artifact + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy run tools import '$inputs' @@ -64,6 +67,16 @@ write(json.dumps(inputs)) + + + + + + + + + + @@ -78,12 +91,9 @@ write(json.dumps(inputs)) - - - @@ -99,12 +109,15 @@ write(json.dumps(inputs)) + - + + + @@ -118,6 +131,15 @@ write(json.dumps(inputs)) + + + + + + + + + @@ -127,7 +149,6 @@ write(json.dumps(inputs)) - @@ -139,6 +160,8 @@ write(json.dumps(inputs)) + + @@ -149,6 +172,7 @@ write(json.dumps(inputs)) + @@ -306,6 +330,136 @@ write(json.dumps(inputs)) + + + + + + +
+ + +
+ + + + + + + + + +
+ + +
+ + + + + + + + + +
+ + +
+ + + + + + + + + +
+ + +
+ + + + + + + + + +
+ + +
+ + + + + + + + + +
+ + +
+ + + + + + + + + +
+ + +
+ + + + + + + + + +
+ + +
+ + + + + + + + + +
+ + +
+ + + + + + + + + +
+ + +
+ + + @@ -619,44 +773,6 @@ write(json.dumps(inputs)) - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - .+\.annotations - - - - - -
- - - @@ -771,82 +887,6 @@ write(json.dumps(inputs)) - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - .+\.annotations - - - - - -
- - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - .+\.annotations - - - - - -
- - - @@ -1152,6 +1192,26 @@ write(json.dumps(inputs)) + + + + + + + +
+ + +
+ + +
+ + +
+ + + @@ -1212,20 +1272,20 @@ write(json.dumps(inputs)) - + - + - -
- + +
+ - + @@ -1239,10 +1299,10 @@ write(json.dumps(inputs)) - - .*\..*\.seed_orthologs + + .+\.(fasta|fa)$ - + @@ -1326,20 +1386,20 @@ write(json.dumps(inputs)) - + - + - -
- + +
+ - + @@ -1353,10 +1413,10 @@ write(json.dumps(inputs)) - - .+\.(fa|faa|fasta)$ + + .+\.annotations - + @@ -1364,18 +1424,94 @@ write(json.dumps(inputs)) - + - + - -
- - -
- - + +
+ + + + + + + + + + + + + + + + + + + + + + .*\..*\.seed_orthologs + + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + .+\.(fa|faa|fasta)$ + + + + + +
+ + + + + + + + + +
+ + +
+ + @@ -1553,6 +1689,195 @@ write(json.dumps(inputs)) + + + + + + +
+ + .*\.hmm + + +
+ + + + + + + + + +
+ + .*\.hmm + + +
+ + + + + + + + + +
+ + .*\.hmm + + +
+ + + + + + + + + +
+ + .*\.hmm\.h3m + + +
+
+ + .*\.hmm\.h3i + + +
+
+ + .*\.hmm\.h3f + + +
+
+ + .*\.hmm\.h3p + + +
+ + + + + + + + + +
+ + .*\.hmm\.h3m + + +
+
+ + .*\.hmm\.h3i + + +
+
+ + .*\.hmm\.h3f + + +
+
+ + .*\.hmm\.h3p + + +
+ + + + + + + + + +
+ + .*\.hmm\.h3m + + +
+
+ + .*\.hmm\.h3i + + +
+
+ + .*\.hmm\.h3f + + +
+
+ + .*\.hmm\.h3p + + +
+ + + + + + + + + +
+ + .*\.hmm + + +
+ + + + + + + + + +
+ + .*\.hmm + + +
+ + + + + + + + + +
+ + .*\.hmm + + +
+ + + @@ -1747,44 +2072,6 @@ write(json.dumps(inputs)) - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - .*\..*\.seed_orthologs - - - - - -
- - - @@ -2318,6 +2605,82 @@ write(json.dumps(inputs)) + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + .+\.annotations + + + + + +
+ + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + .*\..*\.seed_orthologs + + + + + +
+ + + @@ -2858,6 +3221,19 @@ write(json.dumps(inputs)) + + + + + + +
+ + +
+ + + @@ -2924,10 +3300,36 @@ Formats: -------- These formats have documentation available. -FastqGzFormat -************* +HeaderlessTSVTaxonomyFormat +*************************** +Format for a 2+ column TSV file without a header. -A gzipped fastq file. +This format supports comment lines starting with #, and blank lines. + + +PressedProfileHmmsDirectoryFmt +****************************** + +The <hmmfile>.h3m file contains the profile HMMs +and their annotation in a binary format. The <hmmfile>.h3i file is an +SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains +precomputed data structures for the fast heuristic filter +(the MSV filter). The <hmmfile>.h3p file contains precomputed data +structures for the rest of each profile. + +TSVTaxonomyFormat +***************** +Format for a 2+ column TSV file with an expected minimal header. + +The only header recognized by this format is: + + Feature ID<tab>Taxon + +Optionally followed by other arbitrary columns. + +This format supports blank lines. The expected header must be the first +non-blank line. In addition to the header, there must be at least one line +of data. SampleIdIndexedSingleEndPerSampleDirFmt @@ -2974,13 +3376,6 @@ Format details: - Each sequence must be DNA and cannot be empty. -HeaderlessTSVTaxonomyFormat -*************************** -Format for a 2+ column TSV file without a header. - -This format supports comment lines starting with #, and blank lines. - - SequenceCharacteristicsFormat ***************************** @@ -2995,107 +3390,106 @@ tied to a property. For example the "validate_seq_char_len" validator for "FeatureData[SequenceCharacteristics % Properties("length")]" adds validation for a numerical column called "length". -TSVTaxonomyFormat -***************** -Format for a 2+ column TSV file with an expected minimal header. - -The only header recognized by this format is: - - Feature ID<tab>Taxon - -Optionally followed by other arbitrary columns. +FastqGzFormat +************* -This format supports blank lines. The expected header must be the first -non-blank line. In addition to the header, there must be at least one line -of data. +A gzipped fastq file. Additional formats without documentation: ***************************************** - - DataLoafPackageDirFmt - - EggnogRefDirFmt - - NCBITaxonomyDirFmt - - SILVATaxonomyFormat - - MixedCaseAlignedRNAFASTAFormat - - MAGSequencesDirFmt + - DifferentialFormat - Kraken2OutputDirectoryFormat - - BAMDirFmt - - EggnogProteinSequencesDirFmt - - ImmutableMetadataFormat - - EMPPairedEndCasavaDirFmt - - LSMatFormat - - SingleLanePerSampleSingleEndFastqDirFmt - - AlignedProteinFASTAFormat - - PairedDNASequencesDirectoryFormat - - BooleanSeriesFormat - - MultiplexedPairedEndBarcodeInSequenceDirFmt - - DecontamScoreFormat - - OrthologAnnotationDirFmt - - GenesDirectoryFormat - MultiBAMDirFmt - - BIOMV210Format - - ErrorCorrectionDetailsFmt - - DiamondDatabaseFileFmt - - PairedRNASequencesDirectoryFormat - - DifferentialFormat - - Kraken2DBDirectoryFormat - - DADA2StatsFormat + - FirstDifferencesFormat + - SingleEndFastqManifestPhred33V2 - AlignedDNAFASTAFormat - - ImportanceFormat - - SingleEndFastqManifestPhred33 - - NewickFormat - - MultiplexedFastaQualDirFmt - - SingleLanePerSamplePairedEndFastqDirFmt - - DeblurStatsFmt + - EggnogProteinSequencesDirFmt + - SingleEndFastqManifestPhred64 + - MAGSequencesDirFmt + - ProteinSingleProfileHmmDirectoryFmt - MixedCaseDNAFASTAFormat - - SingleEndFastqManifestPhred33V2 + - ImportanceFormat + - ImmutableMetadataFormat + - ErrorCorrectionDetailsFmt + - ArtificialGroupingFormat + - OrthologAnnotationDirFmt + - DecontamScoreFormat + - SingleEndFastqManifestPhred64V2 - QualityFilterStatsFmt - - SingleEndFastqManifestPhred64 - - MultiFASTADirectoryFormat - - ProcrustesStatisticsFmt + - DeblurStatsFmt + - OrdinationFormat + - PairedEndFastqManifestPhred33 + - LSMatFormat + - ProteinMultipleProfileHmmDirectoryFmt + - SingleLanePerSamplePairedEndFastqDirFmt - CasavaOneEightLanelessPerSampleDirFmt - - SILVATaxidMapFormat - - SingleEndFastqManifestPhred64V2 - - Kraken2ReportDirectoryFormat + - Kraken2DBDirectoryFormat - MixedCaseAlignedDNAFASTAFormat + - MultiplexedFastaQualDirFmt + - BooleanSeriesFormat + - BLASTDBDirFmtV5 + - DADA2StatsFormat - BLAST6Format + - KaijuDBDirectoryFormat + - MultiFASTADirectoryFormat + - PairedEndFastqManifestPhred64 + - MAGtoContigsFormat + - DNASingleProfileHmmDirectoryFmt + - RNAFASTAFormat - ProbabilitiesFormat - - PairedEndFastqManifestPhred33 + - SampleEstimatorDirFmt + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - TableJSONLFileFormat + - LociDirectoryFormat + - PairedEndFastqManifestPhred33V2 + - UchimeStatsFmt + - ProcrustesStatisticsFmt + - AlphaDiversityFormat - MultiMAGSequencesDirFmt + - SeppReferenceDirFmt + - DNAMultipleProfileHmmDirectoryFmt + - PredictionsFormat + - PlacementsFormat + - NewickFormat + - BrackenDBDirectoryFormat + - GenomeSequencesDirectoryFormat + - EggnogRefDirFmt + - PairedEndFastqManifestPhred64V2 + - AlignedRNAFASTAFormat - EMPSingleEndDirFmt - - Bowtie2IndexDirFmt - TaxonomicClassiferTemporaryPickleDirFmt - - LociDirectoryFormat - - ArtificialGroupingFormat - - MAGtoContigsFormat - - BrackenDBDirectoryFormat - - ProteinFASTAFormat - - RNAFASTAFormat - - BIOMV100Format - - Kraken2DBReportFormat - - PairedEndFastqManifestPhred64 + - Kraken2ReportDirectoryFormat - MultiBowtie2IndexDirFmt - - EMPPairedEndDirFmt - - OrdinationFormat + - SILVATaxidMapFormat + - CasavaOneEightSingleLanePerSampleDirFmt + - RNASingleProfileHmmDirectoryFmt + - MixedCaseRNAFASTAFormat + - Bowtie2IndexDirFmt - SeedOrthologDirFmt - - SampleEstimatorDirFmt - - PlacementsFormat - - DNAFASTAFormat - - UchimeStatsFmt - - PairedEndFastqManifestPhred33V2 - - AlignedRNAFASTAFormat - - KaijuDBDirectoryFormat + - DiamondDatabaseFileFmt + - ProteinFASTAFormat + - EMPPairedEndDirFmt - ContigSequencesDirFmt + - Kraken2DBReportFormat + - RNAMultipleProfileHmmDirectoryFmt + - SILVATaxonomyFormat + - BIOMV100Format + - DataLoafPackageDirFmt + - MixedCaseAlignedRNAFASTAFormat - EMPSingleEndCasavaDirFmt - - FirstDifferencesFormat - - SeppReferenceDirFmt - - PredictionsFormat + - DNAFASTAFormat - ProteinsDirectoryFormat - - MixedCaseRNAFASTAFormat - - PairedEndFastqManifestPhred64V2 - - BLASTDBDirFmtV5 - - AlphaDiversityFormat - - CasavaOneEightSingleLanePerSampleDirFmt + - PairedDNASequencesDirectoryFormat + - NCBITaxonomyDirFmt + - BIOMV210Format + - AlignedProteinFASTAFormat + - SingleLanePerSampleSingleEndFastqDirFmt + - EMPPairedEndCasavaDirFmt + - BAMDirFmt + - PairedRNASequencesDirectoryFormat + - GenesDirectoryFormat + - SingleEndFastqManifestPhred33 10.1038/s41587-019-0209-9 diff --git a/tools/suite_qiime2_core__tools/qiime2_core__tools__import_fastq.xml b/tools/suite_qiime2_core__tools/qiime2_core__tools__import_fastq.xml index 13343e4..0f94253 100644 --- a/tools/suite_qiime2_core__tools/qiime2_core__tools__import_fastq.xml +++ b/tools/suite_qiime2_core__tools/qiime2_core__tools__import_fastq.xml @@ -6,14 +6,17 @@ Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> - + Import fastq data into a QIIME 2 artifact + + qiime2 + - quay.io/qiime2/amplicon:2024.5 + quay.io/qiime2/amplicon:2024.10 q2galaxy run tools import-fastq '$inputs'