Mercurial > repos > iuc > mothur_deunique_tree

diff deunique.tree.xml @ 4:97224f81d194 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author: iuc
date: Wed, 14 Feb 2018 09:57:25 -0500
parents: 3ee6e1eab975
children: 24635ce930ee
--- a/deunique.tree.xml	Fri Sep 08 13:06:47 2017 -0400
+++ b/deunique.tree.xml	Wed Feb 14 09:57:25 2018 -0500
@@ -7,19 +7,19 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$tree" tree.dat &&
-        ln -s "$names" names.dat &&
+## create symlinks to input datasets
+ln -s '$tree' tree.dat &&
+ln -s '$names' names.dat &&
 
-        echo 'deunique.tree(
-            tree=tree.dat,
-            name=names.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'deunique.tree(
+    tree=tree.dat,
+    name=names.dat
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="tree" type="data" format="mothur.tre" label="tree - Sequences to filter"/>
@@ -37,8 +37,7 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -52,7 +51,6 @@
 
 v1.21.0: Updated to Mothur 1.33
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>