Initial commit for i2nca #777
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added 30 commits
July 2, 2024 22:11
bgruening
reviewed
Oct 14, 2024
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| <tool id="i2nca_agnostic_qc" name="i2nca Agnostic QC Report " version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> | |||
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please use the Galaxy Language Server and reformat those tools, so that indentation matches etc ...
| </requirements> | ||
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| <command detect_errors="exit_code"><![CDATA[ | ||
| cp "${infile.extra_files_path}/imzml" indata.imzML && |
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please use single quotes everywhere
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| <citation type="bibtex"> | ||
| @article{10.1093/gigascience/giab049, | ||
| author = {Cordes, Jonas and Enzlein, Thomas and Marsching, Christian and Hinze, Marven and Engelhardt, Sandy and Hopf, Carsten and Wolf, Ivo}, | ||
| title = "{M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data}", | ||
| journal = {GigaScience}, | ||
| volume = {10}, | ||
| number = {7}, | ||
| year = {2021}, | ||
| month = {07}, | ||
| issn = {2047-217X}, | ||
| doi = {10.1093/gigascience/giab049}, | ||
| url = {https://doi.org/10.1093/gigascience/giab049} | ||
| } | ||
| </citation> |
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Suggested change
| <citation type="bibtex"> | |
| @article{10.1093/gigascience/giab049, | |
| author = {Cordes, Jonas and Enzlein, Thomas and Marsching, Christian and Hinze, Marven and Engelhardt, Sandy and Hopf, Carsten and Wolf, Ivo}, | |
| title = "{M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data}", | |
| journal = {GigaScience}, | |
| volume = {10}, | |
| number = {7}, | |
| year = {2021}, | |
| month = {07}, | |
| issn = {2047-217X}, | |
| doi = {10.1093/gigascience/giab049}, | |
| url = {https://doi.org/10.1093/gigascience/giab049} | |
| } | |
| </citation> | |
| <citation type="doi">10.1093/gigascience/giab049</citation> |
Use the force Luke!
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Why not putting the citations into the macro and not repeat yourself?
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| <requirements> | ||
| <container type="docker">biocontainers/i2nca:0.3.12_cv1</container> | ||
| </requirements> |
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Why not moving this to a macro?
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| <tool id="i2nca_splitter" name="Split a imzML file into smaller files with i2nca" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> | |||
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please add to all tools a "profile='23.0'" can also be macrofied ...
| mv ./outdata_B.ibd "${os.path.join($outfile_b.files_path, 'outfile_B.ibd')}" | true && | ||
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| echo "imzML A:" > $outfile_a && | ||
| ls -l "$outfile_a.files_path" >> $outfile_a && |
| <data format="imzml" name="outfile_a" label="ROI A imzML, Conversion result of ${on_string}: imzML"/> | ||
| <data format="imzml" name="outfile_b" label="ROI B imzML, Conversion result of ${on_string}: imzML"/> | ||
| </outputs> | ||
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| ]]></help> | ||
| <citations> | ||
| <citation type="bibtex"> |
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i2nca is a preprocessing software for MSI data in imzML format. Tools for conversion, QC reports and multi-file operations are included.
I am having some issues with collecting a dataset collection of the composite file imzML, so probably not all tools will work right away.