Mercurial > repos > bzonnedda > conifer2

changeset 12:dd24e1e47bbb draft

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Uploaded
author bzonnedda
date Mon, 20 Feb 2017 06:57:07 -0500
parents 13d57b28ee27
children 09ef072c4070
files c_rpkm.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/c_rpkm.xml	Mon Feb 20 06:45:41 2017 -0500
+++ b/c_rpkm.xml	Mon Feb 20 06:57:07 2017 -0500
@@ -1,19 +1,19 @@
 <tool id="conifer_rpkm" name="CoNIFER RPKM and Analyze" version="1.0">
   <description></description>
-  <command>
+  <command interpreter="bash">
      mkdir rpkm_dir;
 #for $input_bam in $inputs:
 	#if str($input_bam.label.value) != "":
 	     ln -s ${input_bam.inputFile} ${$input_bam.label.value}.bam;
 	     ln -s ${input_bam.inputFile.metadata.bam_index} ${$input_bam.label.value}.bam.bai;
-	     python conifer.py rpkm 
+	     python ./conifer.py rpkm 
 	     --probes $probesFile 
 	     --input ${$input_bam.label.value}.bam
 	     --output rpkm_dir/${$input_bam.label.value}.txt;
 	#else
 	     ln -s ${input_bam.inputFile} ${input_bam.inputFile.dataset.name}.bam;
 	     ln -s ${input_bam.inputFile.metadata.bam_index} ${input_bam.inputFile.dataset.name}.bam.bai;
-	     python conifer.py rpkm 
+	     python ./conifer.py rpkm 
 	     --probes $probesFile 
 	     --input ${input_bam.inputFile.dataset.name}.bam
 	     --output rpkm_dir/${input_bam.inputFile.dataset.name}.txt;