diff summary.qual.xml @ 0:41f5224b856b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/summary.qual.xml	Fri May 19 05:00:52 2017 -0400
@@ -0,0 +1,59 @@
+<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="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## 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 $count:
+                ,count=count.dat
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
+        <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_summary" format="mothur.summary" from_work_dir="qfile*.summary" label="${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 Documentation**
+
+The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information.
+
+.. _summary.qual: https://www.mothur.org/wiki/Summary.qual
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>