Mercurial > repos > bebatut > sortmerna

diff sortmerna.xml @ 12:bf5dbe8f7d4c draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 86b25c80bf4746a0bb73002040487242048a40d2-dirty
author bebatut
date Tue, 10 Nov 2015 04:05:25 -0500
parents b8ba70feb088
children 4016c1db6886
line wrap: on
line diff
--- a/sortmerna.xml	Fri Nov 06 04:40:46 2015 -0500
+++ b/sortmerna.xml	Tue Nov 10 04:05:25 2015 -0500
@@ -11,7 +11,7 @@
 
     <version_command>
 <![CDATA[
-sortmerna --version 2>&1|grep 'SortMeRNA version'
+\${SORTMERNADIR}/sortmerna --version 2>&1|grep 'SortMeRNA version'
 ]]>
     </version_command>
 
@@ -34,11 +34,11 @@
         #end for
     #end if
 
-    indexdb_rna --ref $ref -L $seed_length --max_pos $max_pos
+    \${SORTMERNADIR}/indexdb_rna --ref $ref -L $seed_length --max_pos $max_pos
 
     &&
 
-    sortmerna
+    \${SORTMERNADIR}/sortmerna
         --ref $ref
         --reads $input_sequence_file
         --aligned aligned