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

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
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--- a/qiime2/qiime_vsearch_cluster-features-open-reference.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_vsearch_cluster-features-open-reference.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,54 +1,65 @@
 <?xml version="1.0" ?>
-<tool id="qiime_vsearch_cluster-features-open-reference" name="qiime vsearch cluster-features-open-reference" version="2019.7">
-	<description> -  Open-reference clustering of features.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_vsearch_cluster-features-open-reference" name="qiime vsearch cluster-features-open-reference"
+      version="2020.8">
+  <description> Open-reference clustering of features.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime vsearch cluster-features-open-reference
 
 --i-sequences=$isequences
+
 --i-table=$itable
+
 --i-reference-sequences=$ireferencesequences
---p-perc-identity="$ppercidentity"
+
+--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-new-reference-sequences=onewreferencesequences
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-cp oclusteredtable.qza $oclusteredtable;
-cp oclusteredsequences.qza $oclusteredsequences;
 cp onewreferencesequences.qza $onewreferencesequences
-	]]></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" min="0" max="1" exclude_min="True" exclude_max="False" value="" type="float"/>
-		<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 ${on_string}: newreferencesequences.qza" name="onewreferencesequences"/>
-	</outputs>
-	<help><![CDATA[
-Open-reference clustering of features.
-######################################
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table.                                    [required]" name="isequences" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered.        [required]" name="itable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The sequences to use as cluster centroids. [required]" name="ireferencesequences" optional="False" type="data" />
+    <param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True)   The percent identity at which clustering should be performed. This parameter maps to vsearch\'s --id parameter.                                [required]" name="ppercidentity" optional="False" type="text" />
+    <param label="--p-strand: " name="pstrand" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="plus">plus</option>
+      <option value="both">both</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${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}: newreferencesequences.qza" name="onewreferencesequences" />
+    
+  </outputs>
+
+  <help><![CDATA[
+ Open-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
@@ -86,6 +97,9 @@
 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
 -------
@@ -97,9 +111,9 @@
     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>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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