Mercurial > repos > devteam > picard

changeset 4:ab1f60c26526 draft

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Uploaded valid tools and complex repository dependency definition.
author devteam
date Fri, 21 Feb 2014 12:07:49 -0500
parents bf1c3f9f8282
children 3d4f1fa26f0e
files rgPicardASMetrics.xml rgPicardGCBiasMetrics.xml tool_dependencies.xml
diffstat 3 files changed, 3 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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>
--- 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>