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changeset 4:c05e34aa939b draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit e5b8f29dde45dddcda6ee283212dd1bdde487f87-dirty
author bebatut
date Fri, 18 Dec 2015 05:05:04 -0500
parents ddc59d42d17c
children 2bf5fcf30e1f
files humann2.xml
diffstat 1 files changed, 5 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/humann2.xml	Fri Dec 18 04:28:22 2015 -0500
+++ b/humann2.xml	Fri Dec 18 05:05:04 2015 -0500
@@ -19,6 +19,10 @@
     </version_command>
 
     <command><![CDATA[
+        (which diamond || exit 200)
+
+        && 
+
         humann2 
             -i "$input_file"
         
@@ -43,7 +47,7 @@
             --metaphlan \${METAPHLAN2_DIR}/
             --metaphlan-options "-t rel_ab"
             --bowtie2 \${PATH}
-            --diamond \${PATH}
+            --diamond `which diamond`
 
             --threads \${GALAXY_SLOTS:-4}