# HG changeset patch
# User devteam
# Date 1471529998 14400
# Node ID ba29251df197aae483268d9ac6319ef977696fa2
# Parent  867a8c8e870e45d3c84d73563af1ab3edc2dd6d8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit b2e1043bf4db38be490fec298a1829f8e4a1c48e

diff -r 867a8c8e870e -r ba29251df197 bowtie_wrapper.py
--- a/bowtie_wrapper.py	Fri Dec 18 18:50:53 2015 -0500
+++ b/bowtie_wrapper.py	Thu Aug 18 10:19:58 2016 -0400
@@ -2,7 +2,6 @@
 
 """
 Runs Bowtie on single-end or paired-end data.
-For use with Bowtie v. 0.12.7
 
 usage: bowtie_wrapper.py [options]
     -t, --threads=t: The number of threads to run
diff -r 867a8c8e870e -r ba29251df197 bowtie_wrapper.xml
--- a/bowtie_wrapper.xml	Fri Dec 18 18:50:53 2015 -0500
+++ b/bowtie_wrapper.xml	Thu Aug 18 10:19:58 2016 -0400
@@ -1,6 +1,6 @@
-<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.4">
+<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.5">
   <requirements>
-    <requirement type="package" version="0.12.7">bowtie</requirement>
+    <requirement type="package" version="1.1.2">bowtie</requirement>
   </requirements>
   <description></description>
   <version_command>bowtie --version</version_command>
@@ -552,7 +552,9 @@
       <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
       <param name="sSettingsType" value="preSet" />
       <param name="suppressHeader" value="true" />
-      <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" />
+      <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True">
+        <metadata name="dbkey" value="equCab2" />
+      </output>
     </test>
     <test>
       <!--
@@ -720,7 +722,9 @@
       <param name="sOffrate" value="-1" />
       <param name="sSeed" value="-1" />
       <param name="suppressHeader" value="true" />
-      <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" />
+      <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True">
+        <metadata name="dbkey" value="equCab2" />
+      </output>
     </test>
     <test>
       <!--
diff -r 867a8c8e870e -r ba29251df197 test-data/bowtie_indices.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bowtie_indices.loc	Thu Aug 18 10:19:58 2016 -0400
@@ -0,0 +1,1 @@
+equCab2chrM	equCab2	Horse (Equus caballus): equCab2 chrM	${__HERE__}/indexes/equCab2chrM/equCab2chrM
diff -r 867a8c8e870e -r ba29251df197 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Thu Aug 18 10:19:58 2016 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the Bowtie mapper format -->
+    <table name="bowtie_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/bowtie_indices.loc" />
+    </table>
+</tables>
diff -r 867a8c8e870e -r ba29251df197 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Dec 18 18:50:53 2015 -0500
+++ b/tool_dependencies.xml	Thu Aug 18 10:19:58 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="bowtie" version="0.12.7">
-        <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="bowtie" version="1.1.2">
+        <repository changeset_revision="8584a4574ab1" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>