Mercurial > repos > dereeper > readseq

changeset 1:36e5445b7807 draft

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Uploaded
author dereeper
date Tue, 08 Jan 2019 10:14:18 -0500
parents 225031d5c818
children bba379e32116
files readseq.xml
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/readseq.xml	Mon Apr 16 08:59:28 2018 -0400
+++ b/readseq.xml	Tue Jan 08 10:14:18 2019 -0500
@@ -17,7 +17,7 @@
 
     <!-- [REQUIRED] The command to execute -->
     <command>
-        readseq $filein -f $format >> $fileout_log 2>&amp;1 &amp;&amp;
+        java -jar /home/galaxy/data/jars/readseq.jar $filein -f $format >> $fileout_log 2>&amp;1 &amp;&amp;
 #if str( $format ) == "1":
  mv ${filein}.ig $fileout
 #elif str( $format ) == "2"  :
@@ -35,7 +35,7 @@
 #elif str( $format ) == "11"  :
  mv ${filein}.phylip2 $fileout
 #elif str( $format ) == "12"  :
- mv ${filein}.phylip $fileout
+ perl $__tool_directory__/complete_names.pl ${filein} ${filein}.phylip $fileout
 #elif str( $format ) == "13"  :
  mv ${filein}.seq $fileout
 #elif str( $format ) == "14"  :