Mercurial > repos > iracooke > tpp_prophets

diff interprophet.xml @ 15:0746a2ae9e04 draft

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:45:24 -0400
parents d90c8bc10a9c
children 1b86e378de37
line wrap: on
line diff
--- a/interprophet.xml	Thu Mar 26 19:55:19 2015 -0400
+++ b/interprophet.xml	Tue Oct 20 20:45:24 2015 -0400
@@ -1,59 +1,71 @@
-<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.0">
-	
-	<requirements>
-         <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>Combine Peptide Prophet results from multiple search engines</description>
-
-  <command>interprophet.rb --galaxy
+<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.1">
+    <description>Combine Peptide Prophet results from multiple search engines</description>
+    <requirements>
+         <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        interprophet.rb --galaxy
+        #if str( $input_type.type ) == "files":
+            #for $pepxml_file in $input_type.pepxml_files:
+                ${pepxml_file}
+            #end for
+        #else
+            #for $list_item in $input_type.pepxml_list:
+                ${list_item}
+            #end for
+            #for $extra_list_holder in $input_type.extra_pepxml_lists:
+                #for $list_item in $extra_list_holder.extra_list:
+                    ${list_item}
+                #end for
+            #end for
+        #end if
 
-	-o interprophet_output.pep.xml
-
-	$use_nss 
-
-	$use_nrs 
-
-	$use_nse 
-
-	$use_nsi 
-
-	$use_nsm 
-
-	--p-thresh $p_thresh
+            -o interprophet_output.pep.xml
+            $use_nss
+            $use_nrs
+            $use_nse
+            $use_nsi
+            $use_nsm
+            --p-thresh $p_thresh
+            --threads "\${GALAXY_SLOTS:-12}"
 
-	--threads $threads
-
-#for $pepxml_file in $pepxml_files:
-	${pepxml_file}
-#end for	
-
-  </command>
-
-
-  <inputs>
-
-	<param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
+]]>
+    </command>
+    <inputs>
 
-	<param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" 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="" 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="" 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="" 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="" falsevalue="--no-nsm"/>
-	
-    <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/>
+        <conditional name="input_type">
+            <param name="type" type="select" label="Input Type">
+                <option value="files" selected="true">Datasets</option>
+                <option value="collections">Collections</option>
+            </param>
+            <when value="files">
+                <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
+            </when>
+            <when value="collections">
+                <param name="pepxml_list" type="data_collection" multiple="true" collection_type="list" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
+                <repeat name="extra_pepxml_lists" title="Additional PepXML Collections" >
+                    <param name="extra_list" type="data_collection" multiple="true" collection_type="list" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
+                </repeat>
+            </when>
+        </conditional>
 
-	<param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/>
-		
-  </inputs>
-  <outputs>
-    <data format="interprophet_pepxml" name="output" label="interprophet.${pepxml_files[0].display_name}" from_work_dir="interprophet_output.pep.xml"/>
-  </outputs>
+        <!-- <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> -->
 
- <help>
+        <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" 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="" 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="" 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="" 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="" falsevalue="--no-nsm"/>
+        <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/>
+
+    </inputs>
+    <outputs>
+        <data format="interprophet_pepxml" name="output" from_work_dir="interprophet_output.pep.xml"/>
+    </outputs>
+    <help>
 
 **What it does**
 
@@ -67,6 +79,5 @@
 
 Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011).
 
-  </help>
-
+    </help>
 </tool>