Mercurial > repos > jjohnson > metaphlan

diff metaphlan.xml @ 1:868624c77941 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add tool_dependencies.xml
author Jim Johnson <jj@umn.edu>
date Tue, 09 Oct 2012 15:53:06 -0500
parents 0ec6c5781381
children 51288d868a5c
line wrap: on
line diff
--- a/metaphlan.xml	Tue Oct 09 12:13:27 2012 -0400
+++ b/metaphlan.xml	Tue Oct 09 15:53:06 2012 -0500
@@ -1,13 +1,14 @@
-<tool id="metaphlan" name="MetaPhlAn" version="1.6.0">
+<tool id="metaphlan" name="MetaPhlAn" version="1.7.0">
 <requirements>
-<requirement type="package">metaphlan</requirement>
-<requirement type="package">bowtie2</requirement>
+    <requirement type="set_environment">METAPHLAN_BASE</requirement>
+    <requirement type="package" version="1.7.0">metaphlan</requirement>
+    <requirement type="package">bowtie2</requirement>
 </requirements>
   <description>Metagenomic Phylogenetic Analysis</description>
   <command>
 	  metaphlan.py 
 	  $input  
-	  --bowtie2db ${GALAXY_DATA_INDEX_DIR}/shared/metaphlan/bowtie2db/mpa  
+	  --bowtie2db ${METAPHLAN_BASE}/bowtie2db/mpa  
 	  --no_map  
 	  -o $output  
 	  --bt2_ps $PresetsForBowtie2