# HG changeset patch
# User bzonnedda
# Date 1499336952 14400
# Node ID 02091c92f4f1c89894508751dd7b65da082c8e5a
# Parent  cbe4551cdc277c54f83920f462d38c3b55c7b4ca
Uploaded

diff -r cbe4551cdc27 -r 02091c92f4f1 c_rpkm.xml
--- a/c_rpkm.xml	Thu Jul 06 06:28:47 2017 -0400
+++ b/c_rpkm.xml	Thu Jul 06 06:29:12 2017 -0400
@@ -1,25 +1,29 @@
-<tool id="conifer_rpkm" name="CoNIFER RPKM and Analyze" version="1.0">
+<tool id="conifer_rpkm" name="CoNIFER RPKM and Analyze" version="1.7">
   <description></description>
+<requirements>
+    <requirement type="package" version="0.10.0">pysam</requirement>
+    <requirement type="package" version="3.3.0">pytables</requirement>
+</requirements>
   <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 '$__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