Mercurial > repos > iracooke > protk
view omssa.xml @ 3:255b5b6ec617 draft default tip
Better defaults for omssa
author | Ira Cooke <iracooke@gmail.com> |
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date | Mon, 23 Jul 2012 14:48:31 +1000 |
parents | 418f42b34049 |
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<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.0"> <requirements> <requirement type="package">protk</requirement> </requirements> <description>Run an OMSSA MS/MS Search</description> <command>#if $database.source_select=="built_in": omssa_search.rb -d $database.dbkey #else #omssa_search.rb -d $database.fasta_file #end if --var-mods=' $variable_mods ' --fix-mods=' $fixed_mods ' --searched-ions=' $searched_ions ' $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol --num-peaks-for-multi-isotope-search $multi_isotope $use_average_mass $respect_precursor_charges --max-hit-expect $max_hit_expect --intensity-cut-off $intensity_cut_off </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">Uploaded fasta 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="mgf" multiple="false" label="MSMS File" help="An mgf 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="omssa_mods.loc"> <column name="name" index="0" /> <column name="value" index="2" /> </options> </param> <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="omssa_mods.loc"> <column name="name" index="0" /> <column name="value" index="2" /> </options> </param> <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">Trypsin</option> <option value="1">Arg-C</option> <option value="2">CNBr</option> <option value="3">Chymotrypsin (FYWL)</option> <option value="4">Formic Acid</option> <option value="5">Lys-C</option> <option value="6">Lys-C, no P rule</option> <option value="7">Pepsin A</option> <option value="8">Trypsin+CNBr</option> <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option> <option value="10">Trypsin, no P rule</option> <option value="11">Whole protein</option> <option value="12">Asp-N</option> <option value="13">Glu-C</option> <option value="14">Asp-N+Glu-C</option> <option value="15">Top-Down</option> <option value="16">Semi-Tryptic</option> <option value="17">No Enzyme</option> <option value="18">Chymotrypsin, no P rule (FYWL)</option> <option value="19">Asp-N (DE)</option> <option value="20">Glu-C (DE)</option> <option value="21">Lys-N (K)</option> <option value="22">Thermolysin, no P rule</option> <option value="23">Semi-Chymotrypsin (FYWL)</option> <option value="24">Semi-Glu-C</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="max_hit_expect" help="Expect values less than this are considered to be hits. Use a large value, eg 10000 when results will be processed downstream with Peptide Prophet" type="float" value="10000.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he--> <param name="intensity_cut_off" help="Peak intensity cut-off as a fraction of maximum peak intensity" type="float" value="0.0005" min="0" max="1" label="Peak intensity cut-off"/><!-- -ci--> <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="use_average_mass" type="boolean" label="Use average precursor masses" help="Match precursor to average mass of the parent ion instead of its monoisotopic mass" truevalue="-a average" falsevalue=""/> <param name="respect_precursor_charges" type="boolean" label="Respect precursor charges" help="Use precursor charge information in input file rather than OMSSA's inferred value" truevalue="--respect-charges" falsevalue=""/> <param name="multi_isotope" type="select" format="text" help="Include this many neighbouring peaks when searching for a match to the precursor mass. Only used when doing monoisotopic search"> <label>Multi-isotope search.</label> <option value="0">0</option> <option value="1">1</option> <option value="2">2</option> <option value="3">3</option> <option value="4">4</option> </param> <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help=""> <option selected="true" value="0">a</option> <option selected="true" value="1">b</option> <option value="2">c</option> <option selected="true" value="3">x</option> <option selected="true" value="4">y</option> <option value="5">zdot</option> <option value="10">adot</option> <option value="11">x-CO2</option> <option value="12">adot-CO2</option> </param> </inputs> <outputs> <data format="raw_pepxml" name="output" metadata_source="input_file" label="omssa_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.pepXML"/> </outputs> <help> **What it does** Runs an MS/MS database search using the OMSSA search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores. ---- **Citation** If you use this tool please read and cite the paper describing OMSSA. Geer L. Y., et al. “Open mass spectrometry search algorithm” *J. Proteome Res.* 3(5), 958-964 (2004). </help> </tool>