comparison tandem.xml @ 14:9d6e0ad4d600 draft

Docker support and update for protk 1.4

13:c60d1f18fd85

<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.2">

   <requirements>
	    <requirement type="package" version="1.3.0">protk</requirement>
   </requirements>

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

	<command>

		-v $missed_cleavages 

		-f $fragment_ion_tol 

		-p $precursor_ion_tol 

		$allow_multi_isotope_search 

		$acetyl_protein_nterm

				<option value="input_ref">Custom parameter file</option>
			</param>
			<when value="built_in">
				<param name="paramskey" type="select" format="text" >
					<label>Paramset</label>
				    <option value="gpm">GPM</option>
				    <option value="isb_native">ISB Native</option>		
					<option value="isb_kscore">ISB K-Score</option>
				</param>
			</when>
			<when value="input_ref">
				<param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
			</when>

		<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="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/>

		<param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>

		<param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/>
		
		<param name="enzyme" type="select" format="text">
		    <label>Enzyme</label>
			<option value="[R]|{P}">argc - [R]|{P}</option>
			<option value="[X]|[D]">aspn - [X]|[D]</option>
			<option value="[FLMWY]|{P}">chymotrypsin - [FLMWY]|{P}</option>
			<option value="[R]|[X]">clostripain - [R]|[X]</option>
			<option value="[M]|{P}">cnbr - [M]|{P}</option>
			<option value="[AGILV]|{P}">elastase - [AGILV]|{P}</option>
			<option value="[D]|{P}">formicacid - [D]|{P}</option>
			<option value="[DE]|{P}">gluc - [DE]|{P}</option>
			<option value="[E]|{P}">gluc_bicarb - [E]|{P}</option>
			<option value="[W]|[X]">iodosobenzoate - [W]|[X]</option>
			<option value="[K]|{P}">lysc - [K]|{P}</option>
			<option value="[K]|[X]">lysc-p - [K]|[X]</option>
			<option value="[X]|[K]">lysn - [X]|[K]</option>
			<option value="[X]|[AKRS]">lysn_promisc - [X]|[AKRS]</option>
			<option value="[X]|[X]">nonspecific - [X]|[X]</option>
			<option value="[FL]|[X]">pepsina - [FL]|[X]</option>
			<option value="[P]|[X]">protein_endopeptidase - [P]|[X]</option>
			<option value="[E]|[X]">staph_protease - [E]|[X]</option>
			<option value="[FMWY]|{P},[KR]|{P},[X]|[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
			<option value="[KR]|{P}" selected="true">trypsin - [KR]|{P}</option>
			<option value="[FKLMRWY]|{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
			<option value="[KR]|{P},[M]|{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
			<option value="[DEKR]|{P}">trypsin_gluc - [DEKR]|{P}</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=""/>

	</inputs>


	<outputs>
		<data format="tandem" 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}.tandem"/>
	</outputs>


  <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.

14:9d6e0ad4d600

<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.0">

   <requirements>
         <container type="docker">iracooke/protk-1.4.1</container>
	    <requirement type="package" version="1.4">protk</requirement>
   </requirements>

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

	<command>

		-v $missed_cleavages 

		-f $fragment_ion_tol 

		-p $precursor_ion_tol

		$allow_multi_isotope_search 

		$acetyl_protein_nterm

				<option value="input_ref">Custom parameter file</option>
			</param>
			<when value="built_in">
				<param name="paramskey" type="select" format="text" >
					<label>Paramset</label>
					<option value="isb_kscore">ISB K-Score (Recommended for TPP)</option>
				    <option value="isb_native">ISB Native</option>		
				    <option value="gpm">GPM</option>
				</param>
			</when>
			<when value="input_ref">
				<param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
			</when>

		<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 selected="true" value="2">2</option>
		</param>

		<param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/>

		<param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>

		<param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/>
		
		<param name="enzyme" type="select" format="text">
		    <label>Enzyme</label>
			<option value="[R]__pc__{P}">argc - [R]|{P}</option>
			<option value="[X]__pc__[D]">aspn - [X]|[D]</option>
			<option value="[FLMWY]__pc__{P}">chymotrypsin - [FLMWY]|{P}</option>
			<option value="[R]__pc__[X]">clostripain - [R]|[X]</option>
			<option value="[M]__pc__{X}">cnbr - [M]|{X}</option>
			<option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option>
			<option value="[D]__pc__{P}">formicacid - [D]|{P}</option>
			<option value="[DE]__pc__{P}">gluc - [DE]|{P}</option>
			<option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option>
			<option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option>
			<option value="[K]__pc__{P}">lysc - [K]|{P}</option>
			<option value="[K]__pc__[X]">lysc-p - [K]|[X]</option>
			<option value="[X]__pc__[K]">lysn - [X]|[K]</option>
			<option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option>
			<option value="[X]__pc__[X]">nonspecific - [X]|[X]</option>
			<option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option>
			<option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option>
			<option value="[E]__pc__[X]">staph_protease - [E]|[X]</option>
			<option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
			<option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option>
			<option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
			<option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
			<option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option>
		</param>

		
		<param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>

		<param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" 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="--multi-isotope-search" falsevalue=""/>

	</inputs>


	<outputs>
		<data format="tandem" 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}.tandem"/>
	</outputs>

	<tests>
		<!-- Just test that the tool runs and produces vaguely correct output -->
		<test>
		    <param name="source_select" value="input_ref"/>
		    <param name="fasta_file" value="testdb.fasta" format="fasta"/>
		    <param name="input_file" value="tiny.mzML" format="mzml"/>
		    <output name="output" format="tandem">
		        <assert_contents>
					<has_text text="tandem-style" />
		        </assert_contents>
		    </output>
		</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.