# HG changeset patch
# User rnateam
# Date 1423752415 18000
# Node ID 12fc62b7dc09fe74a9a6abe2b465070a17a29433
# Parent  af18bb0baa9201d8a84e0af1c477389b035dcafc
Uploaded

diff -r af18bb0baa92 -r 12fc62b7dc09 mapper.xml
--- a/mapper.xml	Tue Jan 27 09:06:06 2015 -0500
+++ b/mapper.xml	Thu Feb 12 09:46:55 2015 -0500
@@ -73,7 +73,7 @@
             #if $operation.refGenomeSource.genomeSource == "history"
                 custom_bowtie_indices
             #else
-                $index
+                $operation.refGenomeSource.index
             #end if
 
             $operation.map_mismatch
diff -r af18bb0baa92 -r 12fc62b7dc09 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jan 27 09:06:06 2015 -0500
+++ b/tool_dependencies.xml	Thu Feb 12 09:46:55 2015 -0500
@@ -1,53 +1,53 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="perl" version="5.18.1">
-      <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="bowtie" version="0.12.7">
-      <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="mirdeep2_mapper" version="2.0">
-      <install version="1.0">
-          <actions>
-              <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action>
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action>
                 <action type="move_file">
-                  <source>clip_adapters.pl</source>
+                    <source>clip_adapters.pl</source>
                     <destination>$INSTALL_DIR</destination>
                 </action>
                 <action type="move_file">
-                  <source>collapse_reads_md.pl</source>
+                    <source>collapse_reads_md.pl</source>
                     <destination>$INSTALL_DIR</destination>
                 </action>
                 <action type="move_file">
-                  <source>convert_bowtie_output.pl</source>
+                    <source>convert_bowtie_output.pl</source>
                     <destination>$INSTALL_DIR</destination>
                 </action>
                 <action type="move_file">
-                  <source>fastaparse.pl</source>
+                    <source>fastaparse.pl</source>
                     <destination>$INSTALL_DIR</destination>
                 </action>
                 <action type="move_file">
-                  <source>fastq2fasta.pl</source>
+                    <source>fastq2fasta.pl</source>
                     <destination>$INSTALL_DIR</destination>
                 </action>
                 <action type="move_file">
-                  <source>illumina_to_fasta.pl</source>
+                    <source>illumina_to_fasta.pl</source>
                     <destination>$INSTALL_DIR</destination>
                 </action>
                 <action type="move_file">
-                  <source>mapper.pl</source>
+                    <source>mapper.pl</source>
                     <destination>$INSTALL_DIR</destination>
                 </action>
                 <action type="move_file">
-                  <source>parse_mappings.pl</source>
+                    <source>parse_mappings.pl</source>
                     <destination>$INSTALL_DIR</destination>
                 </action>
                 <action type="move_file">
-                  <source>rna2dna.pl</source>
+                    <source>rna2dna.pl</source>
                     <destination>$INSTALL_DIR</destination>
                 </action>
                 <action type="set_environment">
-                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>