Mercurial > repos > iuc > mothur_degap_seqs

diff degap.seqs.xml @ 3:de6d0eaca0ed draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:39:59 -0500
parents 7e334883931c
children 2f615bc86373
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line diff
--- a/degap.seqs.xml	Tue Sep 05 16:40:30 2017 -0400
+++ b/degap.seqs.xml	Wed Feb 14 09:39:59 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 'degap.seqs(
-            fasta=fasta.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'degap.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" label="fasta - Dataset"/>