changeset 0:861265ac8cce draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__vsearch__cluster_features_closed_reference.xml	Mon Aug 29 20:33:51 2022 +0000
@@ -0,0 +1,83 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2022, QIIME 2 development team.
+
+Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
+-->
+<!--
+This tool was automatically generated by:
+    q2galaxy (version: 2022.8.1)
+for:
+    qiime2 (version: 2022.8.1)
+-->
+<tool name="qiime2 vsearch cluster-features-closed-reference" id="qiime2__vsearch__cluster_features_closed_reference" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Closed-reference clustering of features.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version vsearch</version_command>
+    <command detect_errors="aggressive">q2galaxy run vsearch cluster_features_closed_reference '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  The sequences corresponding to the features in table.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[Sequence]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
+        </param>
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The feature table to be clustered.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
+        </param>
+        <param name="reference_sequences" type="data" format="qza" label="reference_sequences: FeatureData[Sequence]" help="[required]  The sequences to use as cluster centroids.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[Sequence]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
+        </param>
+        <param name="perc_identity" type="float" min="1e-06" max="1" value="" label="perc_identity: Float % Range(0, 1, inclusive_start=False, inclusive_end=True)" help="[required]  The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter."/>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="strand" type="select" label="strand: Str % Choices('plus', 'both')" display="radio">
+                <option value="plus" selected="true">plus</option>
+                <option value="both">both</option>
+            </param>
+            <param name="threads" type="integer" min="0" max="256" value="1" label="threads: Int % Range(0, 256, inclusive_end=True)" help="[default: 1]  The number of threads to use for computation. Passing 0 will launch one thread per CPU core."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="clustered_table" format="qza" label="${tool.name} on ${on_string}: clustered_table.qza" from_work_dir="clustered_table.qza"/>
+        <data name="clustered_sequences" format="qza" label="${tool.name} on ${on_string}: clustered_sequences.qza" from_work_dir="clustered_sequences.qza"/>
+        <data name="unmatched_sequences" format="qza" label="${tool.name} on ${on_string}: unmatched_sequences.qza" from_work_dir="unmatched_sequences.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: vsearch cluster-features-closed-reference
+==================================================
+Closed-reference clustering of features.
+
+
+Outputs:
+--------
+:clustered_table.qza: The table following clustering of features.
+:clustered_sequences.qza: The sequences representing clustered features, relabeled by the reference IDs.
+:unmatched_sequences.qza: The sequences which failed to match any reference sequences. This output maps to vsearch's --notmatched parameter.
+
+|  
+
+Description:
+------------
+Given a feature table and the associated feature sequences, cluster the features against a reference database based on user-specified percent identity threshold of their sequences. This is not a general-purpose closed-reference 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 will be inherited from the centroid feature of each cluster. See the vsearch documentation for details on how sequence clustering is performed.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.7717/peerj.2584</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>