# HG changeset patch
# User peterjc
# Date 1417193261 18000
# Node ID 8e1e3a1ecad7612affd41a3aade41b1085826b66
# Parent  8c1a4a771903c8a688dee3faefc0aa7f4a2b2ed7
Uploaded v0.0.2, embeds citation

diff -r 8c1a4a771903 -r 8e1e3a1ecad7 tools/samtools_depad/README.rst
--- a/tools/samtools_depad/README.rst	Tue Apr 15 12:00:11 2014 -0400
+++ b/tools/samtools_depad/README.rst	Fri Nov 28 11:47:41 2014 -0500
@@ -21,7 +21,7 @@
 Manual Installation
 ===================
 
-This expects samtools to be on the $PATH, and was tested using v0.1.19.
+This expects samtools to be on the ``$PATH``, and was tested using v0.1.19.
 
 To install the wrapper copy or move the following files under the Galaxy tools
 folder, e.g. in a ``tools/samtools_depad`` folder:
@@ -35,10 +35,10 @@
 
   <tool file="samtools_depad/samtools_depad.xml" />
 
-If you wish to run the unit tests, also add this to ``tools_conf.xml.sample``
-and move/copy the ``test-data`` files under Galaxy's ``test-data`` folder. Then::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
 
-    $ ./run_functional_tests.sh -id samtools_depad
+    $ ./run_tests.sh -id samtools_depad
 
 That's it.
 
@@ -49,7 +49,8 @@
 ======= ======================================================================
 Version Changes
 ------- ----------------------------------------------------------------------
-v0.0.1  - Initial public release
+v0.0.1  - Initial public release.
+v0.0.2  - Embed samtools citation in the tool XML.
 ======= ======================================================================
 
 
diff -r 8c1a4a771903 -r 8e1e3a1ecad7 tools/samtools_depad/samtools_depad.xml
--- a/tools/samtools_depad/samtools_depad.xml	Tue Apr 15 12:00:11 2014 -0400
+++ b/tools/samtools_depad/samtools_depad.xml	Fri Nov 28 11:47:41 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="samtools_depad" name="Depad SAM/BAM file" version="0.0.1">
+<tool id="samtools_depad" name="Depad SAM/BAM file" version="0.0.2">
     <description>samtools depad</description>
     <requirements>
         <requirement type="binary">samtools</requirement>
@@ -56,4 +56,7 @@
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
     </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp352</citation>
+    </citations>
 </tool>
diff -r 8c1a4a771903 -r 8e1e3a1ecad7 tools/samtools_depad/tool_dependencies.xml
--- a/tools/samtools_depad/tool_dependencies.xml	Tue Apr 15 12:00:11 2014 -0400
+++ b/tools/samtools_depad/tool_dependencies.xml	Fri Nov 28 11:47:41 2014 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="36aa94676939" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>