<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.1">

   <requirements>
    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
    <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
   </requirements>

	<description>Run an X!Tandem Search</description>

	<command>
		#if $database.source_select=="built_in":
		rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.dbkey 
		#else #rvm 1.9.3@protk-1.2.0 do tandem_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 $allow_multi_isotope_search --keep-params-files
		
	</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="tandem_mods.loc">
				<column name="name" index="0" />
				<column name="value" index="2" />
			</options>
		</param>

		<repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
			<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="tandem_mods.loc">
				<column name="name" index="0" />
				<column name="value" index="2" />
			</options>
		</param>

		<repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
			<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="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="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="" falsevalue="--strict-monoisotopic-mass"/>

	</inputs>


	<outputs>
		<data format="raw_pepxml" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/>
	</outputs>

	<tests>
    	<test>
    		<param name="source_select" value="input_ref"/>
	      	<param name="fasta_file" value="bsa.fasta"/>
   		   	<param name="input_file" value="bsa.mzML"/>
      		<param name="variable_mods" value="15.994915@M"/>
      		<param name="fixed_mods" value="57.021464@C"/>
      		<param name="allow_multi_isotope_search" value="false"/>
      		<output name="output" file="bsa.pepXML" compare="sim_size" delta="100" /> 
    	</test>
  	</tests>


  <help>

**What it does**

Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.

----

**References**

Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.

  </help>

</tool>