# HG changeset patch
# User devteam
# Date 1415645930 18000
# Node ID aceaf1d94d2db9f19d948b50a59b4d2d88696418
# Parent  a03a7ee6cdff0563ea43729a10ab5f3917a4e740
Uploaded new version from GH

diff -r a03a7ee6cdff -r aceaf1d94d2d bowtie2_wrapper.xml
--- a/bowtie2_wrapper.xml	Thu Jan 23 12:30:45 2014 -0500
+++ b/bowtie2_wrapper.xml	Mon Nov 10 13:58:50 2014 -0500
@@ -263,7 +263,7 @@
             <param name="source" value="history" />
             <param name="input_1" value="bowtie2/phix_reads.fastq" ftype="fastqsanger"/>
             <param name="own_file" value="bowtie2/phix_genome.fasta" />
-            <output name="output" file="bowtie2/phix_mapped.bam" />
+            <output name="output" file="bowtie2/phix_mapped.bam" ftype="bam" lines_diff="2" />
         </test>
     </tests>
 
diff -r a03a7ee6cdff -r aceaf1d94d2d tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Thu Jan 23 12:30:45 2014 -0500
+++ b/tool_data_table_conf.xml.sample	Mon Nov 10 13:58:50 2014 -0500
@@ -1,7 +1,7 @@
 <!-- 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 Bowtie2 mapper format for TopHat2 to use -->
-    <table name="tophat2_indexes" comment_char="#">
+    <!-- Locations of indexes in the Bowtie2 mapper format -->
+    <table name="bowtie2_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/bowtie2_indices.loc" />
     </table>
diff -r a03a7ee6cdff -r aceaf1d94d2d tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jan 23 12:30:45 2014 -0500
+++ b/tool_dependencies.xml	Mon Nov 10 13:58:50 2014 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="bowtie2" version="2.1.0">
-      <repository changeset_revision="606d435a57a4" name="package_bowtie2_2_1_0" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="606d435a57a4" name="package_bowtie2_2_1_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.18">
-      <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>