# HG changeset patch
# User bzonnedda
# Date 1487591827 18000
# Node ID dd24e1e47bbb4e6ba89ab7c0492e16f048987c61
# Parent  13d57b28ee27d9db5809098e972fee3a7bf8ef86
Uploaded

diff -r 13d57b28ee27 -r dd24e1e47bbb c_rpkm.xml
--- 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;