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diff summary.qual.xml @ 0:b889c8e70a45 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:51:35 -0400
parents
children c6f0d24c9cfe
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/summary.qual.xml	Fri Jun 24 16:51:35 2016 -0400
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+<tool profile="16.07" id="mothur_summary_qual" name="Summary.qual" version="@WRAPPER_VERSION@.0">
+    <description>Summarize the quality scores</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        ## create symlinks to input datasets
+        ln -s "$qfile" qfile.dat &&
+        ln -s "$name" name.dat &&
+        ln -s "$count" count.dat &&
+
+        echo 'summary.qual(
+            qfile=qfile.dat
+            #if $name:
+                ,name=name.dat
+            #end if
+            #if $count:
+                ,count=count.dat
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+    ]]></command>
+    <inputs>
+        <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
+        <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_summary" format="mothur.summary" from_work_dir="qfile*.summary" label="${tool.name} on ${on_string}: summary"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/>
+            <output name="out_summary" md5="04de7c9d0f3889d5e121db9d9070c935"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information.
+
+.. _summary.qual: http://www.mothur.org/wiki/Summary.qual
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>