--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msgfplus_search.xml	Mon Mar 04 20:48:04 2013 -0500
@@ -0,0 +1,140 @@
+<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.0">
+
+	<requirements>
+    	<requirement type="package" version="1.1.9">galaxy_protk</requirement>
+    	<requirement type="package" version="20121116">msgfplus</requirement>
+    	<package name="proteowizard" version="3_0_4388">
+   	</requirements>
+
+
+	<description>Run an MSGF+ Search</description>
+
+	<command>
+		#if $database.source_select=="built_in":
+		rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb --galaxy -d $database.dbkey
+		#else #rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb -d $database.fasta_file
+		#end if
+
+		--var-mods='
+		$variable_mods
+		#for $custom_variable_mod in $custom_variable_mods:
+		,${custom_variable_mod.custom_mod}
+		#end for
+		'
+
+		--fix-mods='
+		$fixed_mods
+		#for $custom_fix_mod in $custom_fix_mods:
+		,${custom_fix_mod.custom_mod}
+		#end for
+		'
+
+		$input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol --instrument=$instrument
+		
+		
+		
+	</command>
+
+	<inputs>	
+		<conditional name="database">
+			<param name="source_select" type="select" label="Database source">
+				<option value="built_in">Built-In</option>
+				<option value="input_ref">Your Upload File</option>
+			</param>
+			<when value="built_in">
+				<param name="dbkey" type="select" format="text" >
+					<label>Database</label>
+					<options from_file="pepxml_databases.loc">
+						<column name="name" index="0" />
+						<column name="value" index="2" />
+					</options>
+				</param>
+			</when>
+			<when value="input_ref">
+				<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
+			</when>
+		</conditional>
+		
+		<param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
+
+
+		<param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
+			clicking to select multiple items">
+			<options from_file="msgfplus_mods.loc">
+				<column name="name" index="0" />
+				<column name="value" index="2" />
+			</options>
+		</param>
+
+		<repeat name="custom_variable_mods" title="Custom Variable Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
+			<param name="custom_mod" type="text">
+			</param>
+		</repeat>
+		
+		
+		<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
+			clicking to select multiple items">
+			<options from_file="msgfplus_mods.loc">
+				<column name="name" index="0" />
+				<column name="value" index="2" />
+			</options>
+		</param>
+
+		<repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
+			<param name="custom_mod" type="text">
+			</param>
+		</repeat>
+		
+		
+
+		<param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
+			<label>Missed Cleavages Allowed</label>
+		    <option value="0">0</option>		
+			<option value="1">1</option>
+			<option value="2">2</option>
+		</param>
+		
+		<param name="enzyme" type="select" format="text">
+		    <label>Enzyme</label>
+		    <option value="Trypsin">Trypsin</option>
+		</param>
+		
+		<param name="instrument" type="select" format="text">
+	    	<label>Instrument Type</label>
+			<option value="2">TOF</option>
+			<option value="0">Low-res LCQ/LTQ</option>
+			<option value="1">High-res LTQ</option>
+		</param>
+
+		<param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
+
+		<param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
+		<param name="precursor_tolu" type="select" format="text">
+		    <label>Precursor Ion Tolerance Units</label>
+		    <option value="ppm">ppm</option>		
+			<option value="Da">Da</option>
+		</param>
+		
+	</inputs>
+
+
+	<outputs>
+		<data format="raw_pepxml" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/>
+	</outputs>
+
+
+  <help>
+
+**What it does**
+
+Runs an MS/MS database search using the MSGFPlus search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
+
+----
+
+**References**
+
+Please see http://proteomics.ucsd.edu/Software/MSGFPlus.html for details of the MSGFPlus search engine and references describing its algorithm
+
+  </help>
+
+</tool>