diff qiime2/qiime_vsearch_cluster-features-closed-reference.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_vsearch_cluster-features-closed-reference.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_vsearch_cluster-features-closed-reference.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,78 +1,78 @@
 <?xml version="1.0" ?>
-<tool id="qiime_vsearch_cluster-features-closed-reference" name="qiime vsearch cluster-features-closed-reference" version="2019.7">
-	<description> -  Closed-reference clustering of features.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<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
 
-#if str($ppercidentity):
-  --p-perc-identity="$ppercidentity"
-#end if
+--p-perc-identity=$ppercidentity
 
 #if str($pstrand) != 'None':
- --p-strand=$pstrand
+--p-strand=$pstrand
 #end if
 
-#set $pthreads = '${GALAXY_SLOTS:-4}'
-
-#if str($pthreads):
- --p-threads="$pthreads"
-#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 oclusteredtable.qza $oclusteredtable;
-cp oclusteredsequences.qza $oclusteredsequences;
 cp ounmatchedsequences.qza $ounmatchedsequences
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table.                                    [required]" name="isequences" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered.        [required]" name="itable" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The sequences to use as cluster centroids. [required]" name="ireferencesequences" optional="False" type="data"/>
-		<param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True)   The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter.                                [required]" name="ppercidentity" optional="False" type="float" value="" min="0" max="1" exclude_max="False" />
-		<param label="--p-strand: " name="pstrand" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="plus">plus</option>
-			<option value="both">both</option>
-		</param>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${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 ${on_string}: unmatchedsequences.qza" name="ounmatchedsequences"/>
-	</outputs>
-	<help><![CDATA[
-Open-reference clustering of features.
-######################################
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table.                                    [required]" name="isequences" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered.        [required]" name="itable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The sequences to use as cluster centroids. [required]" name="ireferencesequences" optional="False" type="data" />
+    <param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True)   The percent identity at which clustering should be performed. This parameter maps to vsearch\'s --id parameter.                                [required]" name="ppercidentity" optional="False" type="text" />
+    <param label="--p-strand: " name="pstrand" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="plus">plus</option>
+      <option value="both">both</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${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. Any sequences that don't match are
-then clustered de novo. This is not a general-purpose 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. For features that match a reference sequence, the centroid feature
-is that reference sequence, so its identifier will become the feature
-identifier. The clustered_sequences result will contain feature
-representative sequences that are derived from the sequences input for all
-features in clustered_table. This will always be the most abundant sequence
-in the cluster. The new_reference_sequences result will contain the entire
-reference database, plus feature representative sequences for any de novo
-features. This is intended to be used as a reference database in subsequent
-iterations of cluster_features_open_reference, if applicable. See the
-vsearch documentation for details on how sequence clustering is performed.
+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
 ----------
@@ -88,20 +88,23 @@
 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]
-    Sequences representing clustered features.
-new_reference_sequences : FeatureData[Sequence]
-    The new reference sequences. This can be used for subsequent runs of
-    open-reference clustering for consistent definitions of features across
-    open-reference feature tables.
-	]]></help>
-<macros>
+    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>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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