annotate omssa.xml @ 8:4294476e3f83 draft default tip

planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty

<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.1.1">
    <description>Run an OMSSA MS/MS Search</description>
    <requirements>
        <container type="docker">iracooke/protk-1.4.3</container>
        <requirement type="package" version="1.4.3">protk</requirement>
        <requirement type="package" version="2.1.9">omssa</requirement>
        <requirement type="package" version="2.2.29">blast+</requirement>
    </requirements>
    <command>omssa_search.rb

        #if $database.source_select=="built_in":
            -d $database.dbkey 
        #else
            -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 selected="true" 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 selected="true" 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="0.5" 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="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="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 value="0">a</option>
            <option selected="true" value="1">b</option>
            <option value="2">c</option>
            <option 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>
    <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="AASequences.fasta" format="fasta"/>
            <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d.mgf" format="mgf"/>
            <param name="max_hit_expect" value="1000"/>
            <param name="precursor_ion_tol" value="1.2"/>
            <param name="precursor_tolu" value="Da"/>
            <param name="fix_mods" value="3"/>
            <param name="variable_mods" value="1"/>


            <output name="output" format="raw_pepxml">
                <assert_contents>
                    <has_text text="VLFSQAQVYELERRFK" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <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>