Mercurial > repos > george-weingart > metaphlan2_hutlab

changeset 12:c7cd6467b570 draft

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Uploaded
author george-weingart
date Mon, 25 Apr 2016 00:47:00 -0400
parents 0e82a9af69ab
children ef38bf0b3208
files metaphlan2_hutlab/metaphlan2.xml
diffstat 1 files changed, 5 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/metaphlan2_hutlab/metaphlan2.xml	Mon Apr 25 00:35:32 2016 -0400
+++ b/metaphlan2_hutlab/metaphlan2.xml	Mon Apr 25 00:47:00 2016 -0400
@@ -3,8 +3,8 @@
 
 	<description>metagenomic profiler V2</description>
 	<command interpreter="python">metaphlan2.py $input 
-		--mpa_pkl   $REPOSITORY_INSTALL_DIR/db_v20/mpa_v20_m200.pkl    
-		--bowtie2db $REPOSITORY_INSTALL_DIR/db_v20/mpa_v20_m200 
+		--mpa_pkl   $METAPHLAN_PATH/db_v20/mpa_v20_m200.pkl    
+		--bowtie2db $METAPHLAN_PATH/db_v20/mpa_v20_m200 
 		--input_type  fastq
 		--no_map 
 		--bt2_ps $PresetsForBowtie2  
@@ -168,7 +168,9 @@
 	 
 
 	</outputs>
-      
+  <requirements>
+    <requirement type="set_environment">METAPHLAN2_PATH</requirement>
+  </requirements>  
   <help>
 **MetaPhlAn**  is a computational tool for profiling the composition of microbial communities *(Bacteria, Archaea, Eukaryotes and Viruses)* from metagenomic shotgun sequencing data with species level resolution.