# HG changeset patch
# User iuc
# Date 1474201269 14400
# Node ID 086edfff112b8f98e85adaf044addb91e7faf061
# Parent  35c1e3785c906ba2a297c522b2d1a41f17803674
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 356a04ca3fb988f20fb63ccf053ef9f62a3d002f

diff -r 35c1e3785c90 -r 086edfff112b data_manager/bowtie_color_space_index_builder.xml
--- a/data_manager/bowtie_color_space_index_builder.xml	Sun Sep 18 07:22:06 2016 -0400
+++ b/data_manager/bowtie_color_space_index_builder.xml	Sun Sep 18 08:21:09 2016 -0400
@@ -1,7 +1,7 @@
-<tool id="bowtie_color_space_index_builder_data_manager" name="Bowtie Color index" tool_type="manage_data" version="0.0.2">
+<tool id="bowtie_color_space_index_builder_data_manager" name="Bowtie Color index" tool_type="manage_data" version="0.0.3">
     <description>builder</description>
     <requirements>
-        <requirement type="package" version="0.12.7">bowtie</requirement>
+        <requirement type="package" version="1.1.2">bowtie</requirement>
     </requirements>
     <command interpreter="python">
         bowtie_index_builder.py
diff -r 35c1e3785c90 -r 086edfff112b data_manager/bowtie_index_builder.py
--- a/data_manager/bowtie_index_builder.py	Sun Sep 18 07:22:06 2016 -0400
+++ b/data_manager/bowtie_index_builder.py	Sun Sep 18 08:21:09 2016 -0400
@@ -32,7 +32,7 @@
     os.symlink( fasta_filename, sym_linked_fasta_filename )
     args = [ 'bowtie-build' ]
     if color_space:
-        args.append( '-c' )
+        args.append( '-C' )
     args.append( sym_linked_fasta_filename)
     args.append( fasta_base_name )
     args.append( sym_linked_fasta_filename )
diff -r 35c1e3785c90 -r 086edfff112b data_manager/bowtie_index_builder.xml
--- a/data_manager/bowtie_index_builder.xml	Sun Sep 18 07:22:06 2016 -0400
+++ b/data_manager/bowtie_index_builder.xml	Sun Sep 18 08:21:09 2016 -0400
@@ -1,7 +1,7 @@
-<tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="0.0.2">
+<tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="0.0.3">
     <description>builder</description>
     <requirements>
-        <requirement type="package" version="0.12.7">bowtie</requirement>
+        <requirement type="package" version="1.1.2">bowtie</requirement>
     </requirements>
     <command interpreter="python">
         bowtie_index_builder.py
diff -r 35c1e3785c90 -r 086edfff112b tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Sep 18 07:22:06 2016 -0400
+++ b/tool_dependencies.xml	Sun Sep 18 08:21:09 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <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" />
+    <package name="bowtie" version="1.1.2">
+        <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>