# HG changeset patch
# User mvdbeek
# Date 1460986894 14400
# Node ID bfeaf4415eba61818f434f1c670acfcc547e505e
# Parent  a39761c27e773a77196c3118e80017f731ae83ab
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 30a73e24eabb05f9d46150fd03471ff853579ad2-dirty

diff -r a39761c27e77 -r bfeaf4415eba sRbowtieParser.xml
--- a/sRbowtieParser.xml	Mon Jun 29 05:54:17 2015 -0400
+++ b/sRbowtieParser.xml	Mon Apr 18 09:41:34 2016 -0400
@@ -1,12 +1,12 @@
-<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.5">
+<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.6">
   <description></description>
   <requirements>
 	<requirement type="package" version="0.12.7">bowtie</requirement>
         <requirement type="package" version="0.7.7">pysam</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
  </requirements>
-<command interpreter="python">
-        sRbowtieParser.py 
+<command>
+        python sRbowtieParser.py
 	          #if $refGenomeSource.genomeSource == "history":
                     --IndexSource $refGenomeSource.ownFile
          	    --ExtractDirective fastaSource
@@ -27,7 +27,7 @@
                   #end for
                   --alignmentLabel          
                   #for $i in $refGenomeSource.input_list
-                    "$i.name"
+                    "$i.element_identifier"
                   #end for
 
 </command>
diff -r a39761c27e77 -r bfeaf4415eba smRtools.pyc
Binary file smRtools.pyc has changed
diff -r a39761c27e77 -r bfeaf4415eba tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jun 29 05:54:17 2015 -0400
+++ b/tool_dependencies.xml	Mon Apr 18 09:41:34 2016 -0400
@@ -7,6 +7,6 @@
       <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="numpy" version="1.9">
-        <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="fc6f5ca8aef3" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>