# HG changeset patch
# User bzonnedda
# Date 1487675022 18000
# Node ID a899c18be1f6b1bec4053822a328581d2ac30d32
# Parent  09ef072c40705d87fecda51cc052f0c307529d88
Uploaded

diff -r 09ef072c4070 -r a899c18be1f6 c_rpkm.xml
--- a/c_rpkm.xml	Tue Feb 21 06:03:27 2017 -0500
+++ b/c_rpkm.xml	Tue Feb 21 06:03:42 2017 -0500
@@ -1,25 +1,25 @@
 <tool id="conifer_rpkm" name="CoNIFER RPKM and Analyze" version="1.0">
   <description></description>
-  <command interpreter="bash">
+  <command>
      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_PATH/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_PATH/conifer.py rpkm 
 	     --probes $probesFile 
 	     --input ${input_bam.inputFile.dataset.name}.bam
 	     --output rpkm_dir/${input_bam.inputFile.dataset.name}.txt;
 	#end if
 #end for
-     python ./conifer.py analyze 
+     python \$CONIFER_PATH/conifer.py analyze 
      --probes $probesFile 
      --rpkm_dir rpkm_dir  
      --output $outputFile