# HG changeset patch
# User bzonnedda
# Date 1499273771 14400
# Node ID 7f685fe845e14a58a84cb2ad414e6cc2a510e659
# Parent  c56e89c84654ed1ec836ab5336c9ca74ff26132b
Uploaded

diff -r c56e89c84654 -r 7f685fe845e1 c_rpkm.xml
--- a/c_rpkm.xml	Thu Feb 23 05:30:31 2017 -0500
+++ b/c_rpkm.xml	Wed Jul 05 12:56:11 2017 -0400
@@ -6,20 +6,20 @@
 	#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_PATH}/conifer.py rpkm 
+	     python '$__tool_directory__/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} ${input_bam.inputFile.dataset.name}.bam.bai;
-	     python \${CONIFER_PATH}/conifer.py rpkm 
+	     python '$__tool_directory__/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_PATH}/conifer.py analyze 
+     python '$__tool_directory__/conifer.py analyze' 
      --probes $probesFile 
      --rpkm_dir rpkm_dir  
      --output $outputFile