# HG changeset patch
# User devteam
# Date 1393002469 18000
# Node ID ab1f60c26526673de0731231d41be23918a3d47f
# Parent  bf1c3f9f8282d7489f1598396986d571175dbf99
Uploaded valid tools and complex repository dependency definition.

diff -r bf1c3f9f8282 -r ab1f60c26526 rgPicardASMetrics.xml
--- a/rgPicardASMetrics.xml	Fri May 03 17:13:01 2013 -0400
+++ b/rgPicardASMetrics.xml	Fri Feb 21 12:07:49 2014 -0500
@@ -26,7 +26,7 @@
       <when value="default">
         <param name="index" type="select" label="Check the assigned reference genome" help="Galaxy thinks that the reads in you dataset were aligned against this reference. If this is not correct, use the 'Select a build-in reference genome' option of the 'Select Reference Genome' dropdown to select approprtiate Reference.">
           <options from_data_table="all_fasta">
-          <filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator="," />
+          <filter type="data_meta" ref="input_file" key="dbkey" column="1" multiple="True" separator="," />
           <validator type="no_options" message="No reference build available for selected input" /> 
           </options>
         </param>
diff -r bf1c3f9f8282 -r ab1f60c26526 rgPicardGCBiasMetrics.xml
--- a/rgPicardGCBiasMetrics.xml	Fri May 03 17:13:01 2013 -0400
+++ b/rgPicardGCBiasMetrics.xml	Fri Feb 21 12:07:49 2014 -0500
@@ -24,7 +24,7 @@
       <when value="default">
         <param name="index" type="select" label="Check the assigned reference genome" help="Galaxy thinks that the reads in you dataset were aligned against this reference. If this is not correct, use the 'Select a build-in reference genome' option of the 'Select Reference Genome' dropdown to select approprtiate Reference.">
           <options from_data_table="all_fasta">
-          <filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/>
+          <filter type="data_meta" ref="input_file" key="dbkey" column="1" multiple="True" separator=","/>
           <validator type="no_options" message="No reference build available for the selected input data" />
           </options>
         </param>
diff -r bf1c3f9f8282 -r ab1f60c26526 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri May 03 17:13:01 2013 -0400
+++ b/tool_dependencies.xml	Fri Feb 21 12:07:49 2014 -0500
@@ -1,19 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="picard" version="1.56.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
-                <action type="move_directory_files">
-                    <source_directory>picard-tools-1.56</source_directory>
-                    <destination_directory>$INSTALL_DIR/jars</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
+        <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>