# HG changeset patch
# User bzonnedda
# Date 1499274175 14400
# Node ID 15d60c7c9a19263720ae1fb3e42326bdffefa7ce
# Parent  7f685fe845e14a58a84cb2ad414e6cc2a510e659
Uploaded

diff -r 7f685fe845e1 -r 15d60c7c9a19 c_rpkm.xml
--- a/c_rpkm.xml	Wed Jul 05 12:56:11 2017 -0400
+++ b/c_rpkm.xml	Wed Jul 05 13:02:55 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 '$__tool_directory__/conifer.py rpkm' 
+	     python '$__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} ${input_bam.inputFile.dataset.name}.bam.bai;
-	     python '$__tool_directory__/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 '$__tool_directory__/conifer.py analyze' 
+     python '$__tool_directory__/conifer.py' analyze 
      --probes $probesFile 
      --rpkm_dir rpkm_dir  
      --output $outputFile