diff qiime2/qiime_vsearch_dereplicate-sequences.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_vsearch_dereplicate-sequences.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_vsearch_dereplicate-sequences.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,10 +1,11 @@
 <?xml version="1.0" ?>
-<tool id="qiime_vsearch_dereplicate-sequences" name="qiime vsearch dereplicate-sequences" version="2019.7">
-	<description> - Dereplicate sequences.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_vsearch_dereplicate-sequences" name="qiime vsearch dereplicate-sequences"
+      version="2020.8">
+  <description>Dereplicate sequences.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime vsearch dereplicate-sequences
 
 --i-sequences=$isequences
@@ -14,22 +15,33 @@
 #end if
 
 --o-dereplicated-table=odereplicatedtable
+
 --o-dereplicated-sequences=odereplicatedsequences
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-cp odereplicatedtable.qza $odereplicatedtable;
 cp odereplicatedsequences.qza $odereplicatedsequences
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality] The sequences to be dereplicated.         [required]" name="isequences" optional="False" type="data"/>
-		<param label="--p-derep-prefix: --p-no-derep-prefix Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant.             [default: False]" name="pderepprefix" selected="False" type="boolean"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: dereplicatedtable.qza" name="odereplicatedtable"/>
-		<data format="qza" label="${tool.name} on ${on_string}: dereplicatedsequences.qza" name="odereplicatedsequences"/>
-	</outputs>
-	<help><![CDATA[
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality] The sequences to be dereplicated.         [required]" name="isequences" optional="False" type="data" />
+    <param label="--p-derep-prefix: --p-derep-prefix: / --p-no-derep-prefix Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant.             [default: False]" name="pderepprefix" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: dereplicatedtable.qza" name="odereplicatedtable" />
+    <data format="qza" label="${tool.name} on ${on_string}: dereplicatedsequences.qza" name="odereplicatedsequences" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Dereplicate sequences.
-######################
+###############################################################
 
 Dereplicate sequence data and create a feature table and feature
 representative sequences. Feature identifiers in the resulting artifacts
@@ -53,9 +65,9 @@
     The table of dereplicated sequences.
 dereplicated_sequences : FeatureData[Sequence]
     The dereplicated sequences.
-	]]></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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