IMP: adds usage example for cluster-features-de-novo

q2_vsearch/_examples.py

@@ -0,0 +1,40 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+from qiime2.plugins import ArtifactAPIUsage
+
+rep_seqs_url = \
+    ('https://s3-us-west-2.amazonaws.com/qiime2-data/2024.2/'
+     'tutorials/chimera/atacama-rep-seqs.qza')
+
+table_url = \
+    ('https://s3-us-west-2.amazonaws.com/qiime2-data/2024.2/'
+     'tutorials/chimera/atacama-table.qza')
+
+use = ArtifactAPIUsage()
+
+
+def cluster_features_de_novo(use):
+    rep_seqs = use.init_artifact_from_url('seqs1', rep_seqs_url)
+    table = use.init_artifact_from_url('table1', table_url)
+
+    perc_identity = 0.97
+    strand = 'plus'
+    threads = 1
+
+    clustered_table, clustered_sequences = use.action(
+        use.UsageAction('vsearch', 'cluster_features_de_novo'),
+        use.UsageInputs(sequences=rep_seqs, table=table,
+                        perc_identity=perc_identity, strand=strand,
+                        threads=threads),
+        use.UsageOutputNames(clustered_table='clustered_table',
+                             clustered_sequences='clustered_sequences')
+    )
+
+    clustered_table.assert_output_type('FeatureTable[Frequency]')
+    clustered_sequences.assert_output_type('FeatureData[Sequence]')

q2_vsearch/plugin_setup.py

@@ -14,6 +14,7 @@
 import q2_vsearch._merge_pairs
 import q2_vsearch._chimera
 import q2_vsearch._stats
+from q2_vsearch._examples import cluster_features_de_novo
 
 from q2_vsearch._type import UchimeStats
 from q2_vsearch._format import UchimeStatsFmt, UchimeStatsDirFmt
@@ -92,7 +93,9 @@
                  '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.')
+                 'on how sequence clustering is performed.'),
+    examples={'cluster_features_de_novo':
+              cluster_features_de_novo}
 )
 
 plugin.methods.register_function(

q2_vsearch/tests/test_examples.py

@@ -0,0 +1,16 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+from qiime2.plugin.testing import TestPluginBase
+
+
+class TestUsageExample(TestPluginBase):
+    package = 'q2_vsearch.tests'
+
+    def test_usage_cluster_features_de_novo(self):
+        self.execute_examples()