Mercurial > repos > iuc > mothur_reverse_seqs

diff reverse.seqs.xml @ 3:8b91c609f0c0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author: iuc
date: Wed, 14 Feb 2018 09:24:53 -0500
parents: 24279ccecac5
children: 876bc0ef523d
--- a/reverse.seqs.xml	Tue Sep 05 16:47:34 2017 -0400
+++ b/reverse.seqs.xml	Wed Feb 14 09:24:53 2018 -0500
@@ -7,17 +7,17 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
 
-        echo 'reverse.seqs(
-            fasta=fasta.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'reverse.seqs(
+    fasta=fasta.dat
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/>
@@ -33,8 +33,7 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -43,7 +42,7 @@
 The reverse.seqs_ command will generate a fasta containing the reverse complement of each sequence in the input fasta.
 
 .. _reverse.seqs: https://www.mothur.org/wiki/Reverse.seqs
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>