MAINT: restore bulk methods through qiime2 independent method

q2_gg2/_cli.py

@@ -0,0 +1,90 @@
+import click
+import qiime2
+import pandas as pd
+from q2_types.tree import NewickFormat
+from q2_types.feature_data import DNAFASTAFormat
+from ._methods import (
+    bulk_sequence_v4_asv_assessment as _bulk_sequence_v4_asv_assessment,
+)
+from ._methods import bulk_clade_v4_asv_assessment as _bulk_clade_v4_asv_assessment
+from ._methods import clade_lookup as _clade_lookup
+
+
+@click.group()
+def cli():
+    pass
+
+
+@cli.command()
+@click.option("--i-taxonomy-as-tree", type=click.Path(exists=True), required=True)
+@click.option("--p-output-filename", type=click.Path(exists=False), required=True)
+@click.option("--p-version", type=str, required=True)
+def clade_lookup(i_taxonomy_as_tree, p_output_filename, p_version):
+    taxonomy_as_tree = qiime2.Artifact.load(i_taxonomy_as_tree).view(NewickFormat)
+    _clade_lookup(taxonomy_as_tree, p_version, p_output_filename)
+
+
+@cli.command()
+@click.option("--i-phylogeny", type=click.Path(exists=True), required=True)
+@click.option("--i-taxa", type=click.Path(exists=True), required=True)
+@click.option("--i-full-length-v4", type=click.Path(exists=True), required=True)
+@click.option("--i-sequences", type=click.Path(exists=True), required=True)
+@click.option("--p-group", type=int, required=True)
+@click.option("--p-output-filename", type=click.Path(exists=False), required=True)
+@click.option("--p-version", type=str, required=True)
+def bulk_clade_v4_asv_assessment(
+    i_phylogeny,
+    i_taxa,
+    i_full_length_v4,
+    i_sequences,
+    p_group,
+    p_output_filename,
+    p_version,
+):
+    phylogeny = qiime2.Artifact.load(i_phylogeny).view(NewickFormat)
+    taxa = qiime2.Artifact.load(i_taxa).view(pd.DataFrame)
+    full_length_v4 = qiime2.Artifact.load(i_full_length_v4).view(DNAFASTAFormat)
+    sequences = qiime2.Artifact.load(i_sequences).view(DNAFASTAFormat)
+    _bulk_clade_v4_asv_assessment(
+        phylogeny,
+        taxa,
+        full_length_v4,
+        sequences,
+        p_version,
+        p_group,
+        p_output_filename,
+    )
+
+
+@cli.command()
+@click.option("--i-phylogeny", type=click.Path(exists=True), required=True)
+@click.option("--i-taxa", type=click.Path(exists=True), required=True)
+@click.option("--i-full-length-v4", type=click.Path(exists=True), required=True)
+@click.option("--i-sequences", type=click.Path(exists=True), required=True)
+@click.option("--o-characterization", type=click.Path(exists=False), required=True)
+@click.option("--p-group", type=int, required=True)
+@click.option("--p-output-filename", type=click.Path(exists=False), required=True)
+@click.option("--p-version", type=str, required=True)
+def bulk_sequence_v4_asv_assessment(
+    i_phylogeny,
+    i_taxa,
+    i_full_length_v4,
+    i_sequences,
+    o_characterization,
+    p_group,
+    p_output_filename,
+    p_version,
+):
+    phylogeny = qiime2.Artifact.load(i_phylogeny).view(NewickFormat)
+    taxa = qiime2.Artifact.load(i_taxa).view(pd.DataFrame)
+    full_length_v4 = qiime2.Artifact.load(i_full_length_v4).view(DNAFASTAFormat)
+    sequences = qiime2.Artifact.load(i_sequences).view(DNAFASTAFormat)
+    _bulk_sequence_v4_asv_assessment(
+        phylogeny,
+        taxa,
+        full_length_v4,
+        sequences,
+        p_version,
+        p_group,
+        p_output_filename,
+    )

setup.py

@@ -21,7 +21,8 @@
     description="Support methods for interaction with Greengenes2",
     entry_points={
         "qiime2.plugins":
-        ["q2-gg2=q2_gg2.plugin_setup:plugin"]
+        ["q2-gg2=q2_gg2.plugin_setup:plugin"],
+        "console_scripts": "greengenes2=q2_gg2._cli:cli"
     },
     package_data={
         'q2_gg2.tests': [],