diff qiime2/qiime_vsearch_cluster-features-de-novo.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_vsearch_cluster-features-de-novo.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_vsearch_cluster-features-de-novo.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,40 +1,50 @@
 <?xml version="1.0" ?>
-<tool id="qiime_vsearch_cluster-features-de-novo" name="qiime vsearch cluster-features-de-novo" version="2019.7">
-	<description> - De novo clustering of features.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_vsearch_cluster-features-de-novo" name="qiime vsearch cluster-features-de-novo"
+      version="2020.8">
+  <description>De novo clustering of features.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime vsearch cluster-features-de-novo
 
 --i-sequences=$isequences
+
 --i-table=$itable
---p-perc-identity="$ppercidentity"
 
-#set $pthreads = '${GALAXY_SLOTS:-4}'
-#if str($pthreads):
- --p-threads="$pthreads"
-#end if
+--p-perc-identity=$ppercidentity
+
+--p-threads=$pthreads
 
 --o-clustered-table=oclusteredtable
+
 --o-clustered-sequences=oclusteredsequences
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-cp oclusteredtable.qza $oclusteredtable;
 cp oclusteredsequences.qza $oclusteredsequences
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table.                                    [required]" name="isequences" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered.        [required]" name="itable" optional="False" type="data"/>
-		
-		<param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True)   The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter.                                [required]" name="ppercidentity" optional="False" min="0" max="1" value="" exclude_min="True" exclude_max="False" type="float"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: clusteredtable.qza" name="oclusteredtable"/>
-		<data format="qza" label="${tool.name} on ${on_string}: clusteredsequences.qza" name="oclusteredsequences"/>
-	</outputs>
-	<help><![CDATA[
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table.                                    [required]" name="isequences" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered.        [required]" name="itable" optional="False" type="data" />
+    <param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True)   The percent identity at which clustering should be performed. This parameter maps to vsearch\'s --id parameter.                                [required]" name="ppercidentity" optional="False" type="text" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: clusteredtable.qza" name="oclusteredtable" />
+    <data format="qza" label="${tool.name} on ${on_string}: clusteredsequences.qza" name="oclusteredsequences" />
+    
+  </outputs>
+
+  <help><![CDATA[
 De novo clustering of features.
-###############################
+###############################################################
 
 Given a feature table and the associated feature sequences, cluster the
 features based on user-specified percent identity threshold of their
@@ -58,15 +68,19 @@
 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.
+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.
-	]]></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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