<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.1">

	<requirements>
    	<requirement type="package" version="1.2.2">galaxy_protk</requirement>
    	<requirement type="package" version="20130227">msgfplus</requirement>
    	<requirement type="package" version="3_0_4388">proteowizard</requirement>
   	</requirements>


	<description>Run an MSGF+ Search</description>

	<command>
		rvm 1.9.3@protk-1.2.2 do msgfplus_search.rb
		#if $database.source_select=="built_in":
		 --galaxy -d $database.dbkey
		#else
		--galaxy -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
		
		--isotope-error-range=$isotope_error_range

		--fragment-method=$fragment_method

		--protocol=$protocol

		--min-pep-len=$min_pep_len
		--max-pep-len=$max_pep_len
		--max-pep-charge=$max_pep_charge
		--min-pep-charge=$min_pep_charge
		--num-reported-matches=$num_reported_matches

		--java-mem=$java_mem

		#if $pepxml_output_use

		#else
		--no-pepxml
		#end if

	</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="Multiple Selection Allowed">
			<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="Multiple Selection Allowed">
			<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="0">unspecific cleavage</option>
		    <option value="1">Trypsin</option>
		    <option value="2">Chymotrypsin</option>
		    <option value="3">Lys-C</option>
		   	<option value="4">Lys-N</option>
			<option value="5">glutamyl endopeptidase</option>
			<option value="6">Arg-C</option>
			<option value="7">Asp-N</option>
			<option value="8">alphaLP</option>
			<option value="9">no cleavage</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_method" type="select" format="text">
	    	<label>Fragmentation Method</label>
			<option value="0">Respect Input File</option>
			<option value="1">CID</option>
			<option value="2">ETD</option>
			<option value="3">HCD</option>
			<option value="4">Merge spectra from same precursor</option>
		</param>

		<param name="protocol" type="select" format="text">
	    	<label>Protocol</label>
			<option value="0">NoProtocol</option>
			<option value="1">Phosphorylation</option>
			<option value="2">iTRAQ</option>
			<option value="3">iTRAQPhospho</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>
		
		<param name="isotope_error_range" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation." type="text" size="80" value="0,1" label="Isotope Error Range"/>

		<param name="min_pep_len" help="" type="integer" value="6" label="Minimum Peptide Length"/>
		<param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/>
		<param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/>
		<param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
		<param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
		<param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/>


		<param name="pepxml_output_use" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />

	</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}.${input_file.display_name}.pepXML"/>
	</outputs>
 -->
	<outputs>
    	<data format="mzid" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}">
      <change_format>
        <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}"/>
      </change_format>
    </data>
  </outputs>


	<tests>
    	<test>
    		<param name="source_select" value="input_ref"/>
	      	<param name="fasta_file" value="bsa.fasta"/>
   		   	<param name="input_file" value="bsa.mzML"/>
      		<output name="output" file="bsa.mzid" compare="sim_size" delta="600" /> 
    	</test>
  	</tests>


  <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>