# HG changeset patch
# User Ira Cooke <iracooke@gmail.com>
# Date 1370783941 18000
# Node ID d19a95abf2e4b0b4273ad3ade8711d5ffdce9dde
# Parent  3f0cb90824f1231bf269200b27b701500432d592
Update

diff -r 3f0cb90824f1 -r d19a95abf2e4 interprophet.xml
--- a/interprophet.xml	Tue Mar 05 00:28:22 2013 -0500
+++ b/interprophet.xml	Sun Jun 09 08:19:01 2013 -0500
@@ -1,17 +1,30 @@
 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.1">
 	
 	<requirements>
-	    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
+	    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
 	    <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
 
 
   <description>Combine Peptide Prophet results from multiple search engines</description>
 
-  <command interpreter="ruby">
+  <command interpreter="bash">
+
+	interprophet_wrapper.sh 
+
+	$output 
+
+	$use_nss 
 
-	interprophet_wrapper.rb $output $use_nss $use_nrs $use_nse $use_nsi $use_nsm --minprob $minprob
+	$use_nrs 
+
+	$use_nse 
 
+	$use_nsi 
+
+	$use_nsm 
+
+	--minprob $minprob
 
 	## Inputs.
 	${first_input}
@@ -29,11 +42,11 @@
 		<param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/>
 	</repeat>
 	
-	<param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--nonss"/>
-	<param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--nonrs"/>
-	<param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--nonse"/>
-	<param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--nonsi"/>
-	<param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--nonsm"/>
+	<param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--no-nss"/>
+	<param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--no-nrs"/>
+	<param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--no-nse"/>
+	<param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--no-nsi"/>
+	<param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--no-nsm"/>
 	
 	<param name="minprob" type="text" label="Minimum threshod probability for reporting results"/>
 		
diff -r 3f0cb90824f1 -r d19a95abf2e4 peptide_prophet.xml
--- a/peptide_prophet.xml	Tue Mar 05 00:28:22 2013 -0500
+++ b/peptide_prophet.xml	Sun Jun 09 08:19:01 2013 -0500
@@ -1,12 +1,29 @@
 <tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.1">
     <requirements>
-        <requirement type="package" version="1.2.0">galaxy_protk</requirement>
+        <requirement type="package" version="1.2.2">galaxy_protk</requirement>
         <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
    
 	<description>Calculate Peptide Prophet statistics on search results</description>
 
-	<command interpreter="ruby">peptide_prophet_wrapper.rb ${output} ${input_file}  -r $glyco $useicat $phospho $usepi $usert $accurate_mass $no_ntt $no_nmc $use_gamma $use_only_expect $force_fit $allow_alt_instruments $maldi
+	<command interpreter="bash">
+        peptide_prophet_wrapper.sh $output $input_file
+
+        -r 
+        $glyco 
+        $useicat 
+        $phospho 
+        $usepi 
+        $usert 
+        $accurate_mass 
+        $no_ntt 
+        $no_nmc 
+        $use_gamma 
+        $use_only_expect 
+        $force_fit 
+        $allow_alt_instruments 
+        $maldi
+
 	</command>
 
 	<inputs>
diff -r 3f0cb90824f1 -r d19a95abf2e4 pepxml_to_table.xml
--- a/pepxml_to_table.xml	Tue Mar 05 00:28:22 2013 -0500
+++ b/pepxml_to_table.xml	Sun Jun 09 08:19:01 2013 -0500
@@ -1,7 +1,7 @@
 <tool id="pepxml_to_table_1" name="PepXML to Table" version="1.0.1">
 
 	<requirements>
-	    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
+	    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
    </requirements>
 
 
@@ -10,12 +10,12 @@
 
 
 <!-- Note .. the input file is assumed to be the first argument -->
-<command>rvm 1.9.3@protk-1.2.0 do pepxml_to_table.rb $input_file -o $output</command>
+<command>rvm 1.9.3@protk-1.2.2 do pepxml_to_table.rb $input_file -o $output</command>
 
 
 <inputs>
 
-	<param name="input_file" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml"  multiple="false" label="Input File" help="A pepXML file"/>
+	<param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml"  multiple="false" label="Input File" help="A pepXML file"/>
 
 </inputs>
 <outputs>
diff -r 3f0cb90824f1 -r d19a95abf2e4 protein_prophet.xml
--- a/protein_prophet.xml	Tue Mar 05 00:28:22 2013 -0500
+++ b/protein_prophet.xml	Sun Jun 09 08:19:01 2013 -0500
@@ -1,6 +1,6 @@
 <tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.1">
 	<requirements>
-	    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
+	    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
 	    <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
 
@@ -8,7 +8,27 @@
 
 
 <!-- Note .. the input file is assumed to be the first argument -->
-  <command interpreter="ruby">protein_prophet_wrapper.rb --galaxy $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command>
+  <command interpreter="bash">
+  	protein_prophet_wrapper.sh 
+
+  	--galaxy $input_file 
+
+  	-r
+
+  	$iproph 
+  	$nooccam 
+  	$groupwts 
+  	$normprotlen 
+  	$logprobs 
+  	$confem 
+  	$allpeps 
+  	$unmapped 
+  	$instances 
+  	$delude
+  	
+  	--minprob=$minprob 
+  	--minindep=$minindep 
+  </command>
   <inputs>
 	
     <param name="input_file" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/>
diff -r 3f0cb90824f1 -r d19a95abf2e4 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Mar 05 00:28:22 2013 -0500
+++ b/repository_dependencies.xml	Sun Jun 09 08:19:01 2013 -0500
@@ -1,10 +1,6 @@
 <?xml version="1.0"?>
 <repositories description="Proteomics datatypes and the TPP">
-
-     <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="dac478a72c1d"/>
-
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349"/>
-
+	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/>
+   	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="e85a18371516"/>
+	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/>
  </repositories>
diff -r 3f0cb90824f1 -r d19a95abf2e4 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Mar 05 00:28:22 2013 -0500
+++ b/tool_dependencies.xml	Sun Jun 09 08:19:01 2013 -0500
@@ -1,12 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
-
-    <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 name="galaxy_protk" version="1.2.2">
+         <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/>
+    </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="e85a18371516"/>
     </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="cedd5e884349" />
-    </package>
-
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>