# HG changeset patch
# User iracooke
# Date 1427414690 14400
# Node ID f567d1818b843eda4e298cfeec7b34ed17b5fb43
# Parent  75184e45bf84a68da70712c9cfe90b97e7665da0
Docker support and update for protk 1.4

diff -r 75184e45bf84 -r f567d1818b84 README
--- a/README	Fri Jun 13 18:26:31 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-This includes tools 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 uses protk which must be installed separately. 
-
-For instructions please see: https://github.com/iracooke/protk/#galaxy-integration
diff -r 75184e45bf84 -r f567d1818b84 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Mar 26 20:04:50 2015 -0400
@@ -0,0 +1,36 @@
+Mascot
+======
+
+Galaxy wrapper for the Mascot_ tandem ms search tool and a tool to convert results to `pepXML`
+
+.. _Mascot: http://www.matrixscience.com/
+
+Requirements
+------------
+
+This package uses protk_, and the trans_proteomic_pipeline_ which need to be present in order for the tool to work.  In addition, you will need a working installation of Mascot_ which is commercial software. 
+
+.. _protk: https://github.com/iracooke/protk
+.. _trans_proteomic_pipeline: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
+
+
+There are two ways you can satify these dependencies (choose one):
+
+1. **Manual Install:** Details on how to install protk_, msgfplus_ and Proteowizard_ manually are available here_.
+
+2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work.  The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed.
+
+.. _docker: https://www.docker.com/
+.. _here: https://github.com/iracooke/protk/#galaxy-integration
+.. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker
+__ container_
+
+
+Further Info
+------------
+
+The source code for this tool and other protk galaxy tools is on github_.  Please visit the github page to contribute to the project or to `report an issue`__ 
+
+.. _github: https://github.com/iracooke/protk-galaxytools
+.. _issue: https://github.com/iracooke/protk-galaxytools/issues
+__ issue_
diff -r 75184e45bf84 -r f567d1818b84 mascot.xml
--- a/mascot.xml	Fri Jun 13 18:26:31 2014 -0400
+++ b/mascot.xml	Thu Mar 26 20:04:50 2015 -0400
@@ -1,7 +1,8 @@
-<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.2">
+<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.0">
 
 	<requirements>
-	    <requirement type="package" version="1.3">protk</requirement>
+            <container type="docker">iracooke/protk-1.4.1</container>
+	    <requirement type="package" version="1.4">protk</requirement>
    </requirements>
 
 	<description>Mascot MS/MS Search</description>
@@ -31,19 +32,26 @@
 		
 		--fix-mods='
 		$fixed_mods
-		'		
-		--allowed-charges=$allowed_charges	
+		'
+
+		--allowed-charges='$allowed_charges'
 
 		--enzyme=$enzyme 
 
-		--instrument=$instrument 
+		--instrument='$instrument'
 
+		-p $precursor_ion_tol
+		
 		--precursor-ion-tol-units=$precursor_tolu 
 
+		#if $email
 		--email=$email 
+		#end if
 
 		-v $missed_cleavages
 
+		--quantitation='$quant_method'
+
 		#if $security.security_use
 		--use-security
 		--username $security.username
@@ -54,6 +62,8 @@
 		--proxy $proxy
 		#end if
 
+		--timeout=600
+
 	</command>
 
 	<inputs>
@@ -63,7 +73,7 @@
 	<conditional name="database">
 		<param name="source_select" type="select" label="Database Type">
 			<option value="built_in">Built-In</option>
-			<option value="custom_defined">Custom</option>
+			<option selected="true" value="custom_defined">Custom</option>
 		</param>
 		<when value="built_in">
 			<param name="dbkey" type="select" format="text" >
@@ -97,7 +107,7 @@
 		<label>Missed Cleavages Allowed</label>
 	    <option value="0">0</option>		
 		<option value="1">1</option>
-		<option value="2">2</option>
+		<option selected="true" value="2">2</option>
 	</param>
 	
 	<param name="enzyme" type="select" format="text">
@@ -143,7 +153,7 @@
 	    <option value="1+, 2+ and 3+">1+,2+ and 3+</option>		
 		<option value="2+">2+</option>
 		<option value="2+ and 3+">2+ and 3+</option>
-		<option value="2+,3+ and 4+">2+,3+ and 4+</option>
+		<option selected="true" value="2+,3+ and 4+">2+,3+ and 4+</option>
 		<option value="3+">3+</option>
 		<option value="4+">4+</option>
 		<option value="5+">5+</option>
@@ -156,7 +166,7 @@
 	    <label>Instrument</label>
 		<option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option>
 		<option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option>
-		<option value="ESI-TRAP">ESI-TRAP</option>
+		<option selected="true" value="ESI-TRAP">ESI-TRAP</option>
 		<option value="ESI-QUAD">ESI-QUAD</option>
 		<option value="ESI-FTICR">ESI-FTICR</option>
 	    <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option>
@@ -168,10 +178,44 @@
 		<option value="MALDI-ISD">MALDI-ISD</option>
 		<option value="CID+ETD">CID+ETD</option>
 	</param>
+
+
+	<param name="quant_method" type="select" format="text">
+	    <label>Quantitation</label>
+		<option selected="true" value="None">None</option>
+		<option value="iTRAQ 4plex">iTRAQ 4plex</option>
+		<option value="iTRAQ 4plex (protein)">iTRAQ 4plex (protein)</option>
+		<option value="iTRAQ 8plex">iTRAQ 8plex</option>
+		<option value="TMT 6plex">TMT 6plex</option>
+		<option value="TMT 2plex">TMT 2plex</option>
+	    <option value="DiLeu 4plex">DiLeu 4plex</option>
+		<option value="18O multiplex">18O multiplex</option>
+		<option value="SILAC K+6 R+6 multiplex">SILAC K+6 R+6 multiplex</option>
+		<option value="IPTL (Succinyl and IMID) multiplex">IPTL (Succinyl and IMID) multiplex</option>
+		<option value="ICPL duplex pre-digest [MD]">ICPL duplex pre-digest [MD]</option>
+		<option value="ICPL duplex post-digest [MD]">ICPL duplex post-digest [MD]</option>
+		<option value="ICPL triplex pre-digest [MD]">ICPL triplex pre-digest [MD]</option>
+		<option value="ICPL quadruplex pre-digest [MD]">ICPL quadruplex pre-digest [MD]</option>
+		<option value="18O corrected [MD]">18O corrected [MD]</option>
+		<option value="15N Metabolic [MD]">15N Metabolic [MD]</option>
+		<option value="15N + 13C Metabolic [MD]">15N + 13C Metabolic [MD]</option>
+		<option value="SILAC K+6 R+10 [MD]">SILAC K+6 R+10 [MD]</option>
+		<option value="SILAC K+6 R+10 Arg-Pro [MD]">SILAC K+6 R+10 Arg-Pro [MD]</option>
+		<option value="SILAC K+6 R+6 [MD]">SILAC K+6 R+6 [MD]</option>
+		<option value="SILAC R+6 R+10 [MD]">SILAC R+6 R+10 [MD]</option>
+		<option value="SILAC K+8 R+10 [MD]">SILAC K+8 R+10 [MD]</option>		
+		<option value="SILAC K+4 K+8 R+6 R+10 [MD]">SILAC K+4 K+8 R+6 R+10 [MD]</option>
+		<option value="ICAT ABI Cleavable [MD]">ICAT ABI Cleavable [MD]</option>
+		<option value="ICAT D8 [MD]">ICAT D8 [MD]</option>
+		<option value="Dimethylation [MD]">Dimethylation [MD]</option>
+		<option value="NBS Shimadzu [MD]">NBS Shimadzu [MD]</option>
+		<option value="Acetylation [MD]">Acetylation [MD]</option>
+		<option value="Label-free [MD]">Label-free [MD]</option>
+	</param>	
 	
-	<param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
+	<param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.5" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
 
-	<param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/>
+	<param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/>
 	<param name="precursor_tolu" type="select" format="text">
 	    <label>Precursor Ion Tolerance Units</label>
 	    <option value="ppm">ppm</option>		
diff -r 75184e45bf84 -r f567d1818b84 mascot_to_pepxml.xml
--- a/mascot_to_pepxml.xml	Fri Jun 13 18:26:31 2014 -0400
+++ b/mascot_to_pepxml.xml	Thu Mar 26 20:04:50 2015 -0400
@@ -1,7 +1,8 @@
-<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.2">
+<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.1.0">
 	<requirements>
-	    <requirement type="package" version="1.3">protk</requirement>
-	    <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement>
+            <container type="docker">iracooke/protk-1.4.1</container>
+	    	<requirement type="package" version="1.4">protk</requirement>
+			<requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
    </requirements>
 
   <description>Converts a mascot results file to pepXML</description>
diff -r 75184e45bf84 -r f567d1818b84 repository_dependencies.xml
--- a/repository_dependencies.xml	Fri Jun 13 18:26:31 2014 -0400
+++ b/repository_dependencies.xml	Thu Mar 26 20:04:50 2015 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="Proteomics datatypes">
-    <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="ac51d9dbfb4d" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
  </repositories>