Mercurial > repos > iracooke > mascot

changeset 4:d9564913a944

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Uploaded
author iracooke
date Tue, 05 Mar 2013 00:18:41 -0500
parents 1747d568a7c8
children 327b2d99d4c5
files README mascot.xml mascot_to_pepxml.xml repository_dependencies.xml tool_dependencies.xml
diffstat 5 files changed, 21 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Tue Mar 05 00:18:41 2013 -0500
@@ -0,0 +1,8 @@
+This package installs wrapper scripts for running Mascot MS/MS searches
+
+Running this tool requires a working installation of Mascot (commercial software).
+Mascot is available from http://www.matrixscience.com/
+
+Requirements:
+This package depends on the galaxy_protk and protk_trans_proteomic_pipeline packages
+Please see instructions for those packages before installing
--- a/mascot.xml	Mon Mar 04 18:40:40 2013 -0500
+++ b/mascot.xml	Tue Mar 05 00:18:41 2013 -0500
@@ -1,14 +1,14 @@
-<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.0">
+<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.1">
 
 
 	<requirements>
-	    <requirement type="package" version="1.1.9">galaxy_protk</requirement>
+	    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
    </requirements>
 
-	<description>Run a Mascot Search on a File</description>
+	<description>Mascot MS/MS Search</description>
 
 
-	<command>rvm 1.9.3@protk-1.1.9 do mascot_search.rb -d $database -f $fragment_ion_tol -S $server $input_file -o $output -r
+	<command>rvm 1.9.3@protk-1.2.0 do mascot_search.rb -d $database -f $fragment_ion_tol -S $server $input_file -o $output -r
 		## Variable Mods
 
 		--var-mods='
--- a/mascot_to_pepxml.xml	Mon Mar 04 18:40:40 2013 -0500
+++ b/mascot_to_pepxml.xml	Tue Mar 05 00:18:41 2013 -0500
@@ -1,12 +1,12 @@
-<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.0">
+<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.1">
 	<requirements>
-	    <requirement type="package" version="1.1.9">galaxy_protk</requirement>
+	    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
 	    <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
 
   <description>Converts a mascot results file to pepXML</description>
 
-<command>rvm 1.9.3@protk-1.1.9 do mascot_to_pepxml.rb $input_file -o $output -d $database</command>
+<command>rvm 1.9.3@protk-1.2.0 do mascot_to_pepxml.rb $input_file -o $output -d $database</command>
 <inputs>
 
 	<param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/>
--- a/repository_dependencies.xml	Mon Mar 04 18:40:40 2013 -0500
+++ b/repository_dependencies.xml	Tue Mar 05 00:18:41 2013 -0500
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <repositories description="Proteomics datatypes and mascot2xml from the TPP">
 
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc"/>
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="463328a6967f"/>
 
-	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/>
+	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/>
 
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="f302406a0297"/>
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349"/>
 
  </repositories>
--- a/tool_dependencies.xml	Mon Mar 04 18:40:40 2013 -0500
+++ b/tool_dependencies.xml	Tue Mar 05 00:18:41 2013 -0500
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
 
-    <package name="galaxy_protk" version="1.1.9">
-	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/>
+    <package name="galaxy_protk" version="1.2.0">
+	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/>
     </package>
 
 	<package name="trans_proteomic_pipeline" version="4.6.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="f302406a0297" />
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349" />
     </package>
 
 </tool_dependency>
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