diff summary.qual.xml @ 2:a40036faabe8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:12:40 -0400
parents 41f5224b856b
children 7afd2d352e05
line wrap: on
line diff
--- a/summary.qual.xml	Tue Sep 05 17:13:19 2017 -0400
+++ b/summary.qual.xml	Tue Mar 20 22:12:40 2018 -0400
@@ -7,30 +7,31 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$qfile" qfile.dat &&
-        ln -s "$name" name.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$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
+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"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -40,11 +41,11 @@
         <test>
             <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/>
             <output name="out_summary" md5="04de7c9d0f3889d5e121db9d9070c935"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -53,7 +54,7 @@
 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>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>