diff qiime2-2020.8/qiime_vsearch_cluster-features-closed-reference.xml @ 20:d93d8888f0b0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_vsearch_cluster-features-closed-reference.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,110 @@
+<?xml version="1.0" ?>
+<tool id="qiime_vsearch_cluster-features-closed-reference" name="qiime vsearch cluster-features-closed-reference"
+      version="2020.8">
+  <description> Closed-reference clustering of features.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime vsearch cluster-features-closed-reference
+
+--i-sequences=$isequences
+
+--i-table=$itable
+
+--i-reference-sequences=$ireferencesequences
+
+--p-perc-identity=$ppercidentity
+
+#if str($pstrand) != 'None':
+--p-strand=$pstrand
+#end if
+
+--p-threads=$pthreads
+
+--o-clustered-table=oclusteredtable
+
+--o-clustered-sequences=oclusteredsequences
+
+--o-unmatched-sequences=ounmatchedsequences
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ounmatchedsequences.qza $ounmatchedsequences
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table.                                    [required]" name="isequences" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered.        [required]" name="itable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The sequences to use as cluster centroids. [required]" name="ireferencesequences" optional="False" type="data" />
+    <param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True)   The percent identity at which clustering should be performed. This parameter maps to vsearch\'s --id parameter.                                [required]" name="ppercidentity" optional="False" type="text" />
+    <param label="--p-strand: " name="pstrand" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="plus">plus</option>
+      <option value="both">both</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: clusteredtable.qza" name="oclusteredtable" />
+    <data format="qza" label="${tool.name} on ${on_string}: clusteredsequences.qza" name="oclusteredsequences" />
+    <data format="qza" label="${tool.name} on ${on_string}: unmatchedsequences.qza" name="ounmatchedsequences" />
+    
+  </outputs>
+
+  <help><![CDATA[
+ Closed-reference clustering of features.
+###############################################################
+
+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.
+
+Parameters
+----------
+sequences : FeatureData[Sequence]
+    The sequences corresponding to the features in table.
+table : FeatureTable[Frequency]
+    The feature table to be clustered.
+reference_sequences : FeatureData[Sequence]
+    The sequences to use as cluster centroids.
+perc_identity : Float % Range(0, 1, inclusive_start=False, inclusive_end=True)
+    The percent identity at which clustering should be performed. This
+    parameter maps to vsearch's --id parameter.
+strand : Str % Choices('plus', 'both'), optional
+    Search plus (i.e., forward) or both (i.e., forward and reverse
+    complement) strands.
+threads : Int % Range(0, 256, inclusive_end=True), optional
+    The number of threads to use for computation. Passing 0 will launch one
+    thread per CPU core.
+
+Returns
+-------
+clustered_table : FeatureTable[Frequency]
+    The table following clustering of features.
+clustered_sequences : FeatureData[Sequence]
+    The sequences representing clustered features, relabeled by the
+    reference IDs.
+unmatched_sequences : FeatureData[Sequence]
+    The sequences which failed to match any reference sequences. This
+    output maps to vsearch's --notmatched parameter.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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