view macros.xml @ 53:d67a3c1bfd09 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424

<macros>
    <import>macros_modifications.xml</import>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Job Failed" />
	    <!--	    <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/>
	    <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
	    <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
	    <regex match="Native memory allocation (malloc) failed" level="fatal_oom" description="Java memory Exception"/>-->
	    <regex match="java.*Exception" level="fatal" description="Java Exception"/>
            <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
	    <regex match="PeptideShaker ran out of memory" level="fatal" description="JVM Error"/>
	    <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
        </stdio>
    </xml>

    <token name="@GENERAL_PARAMETERS@">
            -frag_tol '${precursor_options.fragment_tol}'
            -frag_ppm '${precursor_options.fragment_tol_units}'
            -prec_tol '${precursor_options.precursor_ion_tol}'
            -prec_ppm '${precursor_options.precursor_ion_tol_units}'

            -min_charge $precursor_options.min_charge
            -max_charge $precursor_options.max_charge
            -fi $precursor_options.forward_ion
            -ri $precursor_options.reverse_ion
            -min_isotope ${precursor_options.min_isotope}
            -max_isotope ${precursor_options.max_isotope}
            #if $protein_digest_options.digestion.cleavage == 'default':
              ## -enzyme "Trysin"
              -mc $protein_digest_options.digestion.missed_cleavages
            #elif $protein_digest_options.digestion.cleavage == '0' and len($protein_digest_options.digestion.digests) > 0:
              #set $enzymes = []
              #set $missed_cleavages = []
              ## #set $specificities = []
              #for $i, $digest in enumerate($protein_digest_options.digestion.digests):
                  #silent $enzymes.append(str($digest.enzyme))
                  #silent $missed_cleavages.append(str($digest.missed_cleavages))
                  ## #silent $specificities.append(str($digest.specificity))
              #end for
              -enzyme "#echo ','.join($enzymes)#"
              -mc "#echo ','.join($missed_cleavages)#"
              ## -specificity "#echo ','.join($specificities)#"
            #else:
               -digestion $protein_digest_options.digestion.cleavage
            #end if

            #set $fixed_mods_str = $protein_modification_options.fixed_modifications or ''
            #set $variable_mods_str = $protein_modification_options.variable_modifications or ''
            #if $fixed_mods_str
                -fixed_mods "$fixed_mods_str"
            #end if
            #if $variable_mods_str
                -variable_mods "$variable_mods_str"
            #end if

    </token>

    <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
    <token name="@SEARCHGUI_VERSION@">3.3.10</token>
    <token name="@PEPTIDESHAKER_VERSION@">1.16.36</token>
    <xml name="general_options">

        <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
            <conditional name="digestion">
                <param name="cleavage" type="select" label="Digestion">
                    <option value="0">Select Enzymes</option>
                    <option value="1">Unspecific Cleavage</option>
                    <option value="2">Whole Protein</option>
                </param>
                <when value="0">
                    <repeat name="digests" min="1" title="Enzymes">
                        <param name="enzyme" type="select" label="Enzyme"
                            help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
                            <option value="Trypsin">Trypsin</option>
                            <option value="Trypsin (no P rule)">Trypsin (no P rule)</option>
                            <option value="Arg-C">Arg-C</option>
                            <option value="Arg-C (no P rule)">Arg-C</option>
                            <option value="Arg-N">Arg-N</option>
                            <option value="Glu-C">Glu-C</option>
                            <option value="Lys-C">Lys-C</option>
                            <option value="Lys-C (no P rule)">Lys-C (no P rule)</option>
                            <option value="Lys-N">Lys-N</option>
                            <option value="Asp-N">Asp-N</option>
                            <option value="Asp-N (ambic)">Asp-N (ambic)</option>
                            <option value="Chymotrypsin">Chymotrypsin</option>
                            <option value="Chymotrypsin (no P rule)">Chymotrypsin (no P rule)</option>
                            <option value="Pepsin A">Pepsin A</option>
                            <option value="CNBr">CNBr</option>
                            <option value="Thermolysin">Thermolysin</option>
                            <option value="LysargiNase">LysargiNase</option>
                        </param>
                        <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
                            help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
                        <!--
                        <param name="specificity" type="select" label="Specificity">
                            <option value="0" selected="true">Specific at both termini</option>
                            <option value="1">Semi-Specific - one terminus</option>
                            <option value="2">Specific at the N-terminus only</option>
                            <option value="3">Specific at the C-terminus only</option>
                        </param>
                        -->
                    </repeat>
                </when>
                <when value="1"/>
                <when value="2"/>
            </conditional>
        </section>

        <section name="precursor_options" expanded="false" title="Precursor Options">
            <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
                help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
                <option value="1">Parts per million (ppm)</option>
                <option value="0">Daltons</option>
            </param>
            <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"
                help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
            <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
                help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
                <option value="1">Parts per million (ppm)</option>
                <option value="0" selected="true">Daltons</option>
            </param>
            <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
                help="Provide error value for fragment ions, based on instrument used"/>
            <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
            <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
            <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
                <option value="a">a</option>
                <option value="b" selected="true">b</option>
                <option value="c">c</option>
            </param>
            <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
                <option value="x">x</option>
                <option value="y" selected="true">y</option>
                <option value="z">z</option>
            </param>
            <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
            <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
        </section>

        <section name="protein_modification_options" expanded="false" title="Protein Modification Options">
            <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
                help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
                <expand macro="modifications"/>
            </param>
            <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
                help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">                
                <expand macro="modifications"/>
            </param>
        </section>

    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/1471-2105-12-70</citation>
            <citation type="doi">10.1002/pmic.201000595</citation>
            <citation type="doi">doi:10.1038/nbt.3109</citation>
        </citations>
    </xml>

</macros>