Mercurial > repos > bzonnedda > conifer2

changeset 21:7f685fe845e1 draft

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Uploaded
author bzonnedda
date Wed, 05 Jul 2017 12:56:11 -0400
parents c56e89c84654
children 15d60c7c9a19
files c_rpkm.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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