comparison macros.xml @ 43:7963340ab569 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad

42:9e20c34298e3

<macros>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Job Failed" />
            <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="CompomicsError" level="fatal" description="Compomics Error"/>
        </stdio>
    </xml>
    <token name="@GENERAL_PARAMETERS@">

            -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 $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

                            <option value="Lys-C, no P rule">Lys-C, no P rule</option>
                            <option value="Pepsin A">Pepsin A</option>
                            <option value="Trypsin + CNBr">Trypsin + CNBr</option>
                            <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
                            <option value="Trypsin, no P rule">Trypsin, no P rule</option>
                            <option value="Whole Protein">Whole Protein</option> 
                            <option value="Asp-N">Asp-N</option>
                            <option value="Glu-C">Glu-C</option>
                            <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
                            <option value="Top-Down">Top-Down</option>
                            <option value="Semi-Tryptic">Semi-Tryptic</option>

            <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">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"/>

                <options from_file="searchgui_mods.loc">
                    <column name="name" index="0" />
                    <column name="value" index="0" />
                </options>
            </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">
                <options from_file="searchgui_mods.loc">
                    <column name="name" index="0" />
                    <column name="value" index="0" />
                </options>

43:7963340ab569

<macros>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Job Failed" />
            <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="CompomicsError" level="fatal" description="Compomics Error"/>
        </stdio>
    </xml>
    <token name="@GENERAL_PARAMETERS@">

            -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 $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

                            <option value="Lys-C, no P rule">Lys-C, no P rule</option>
                            <option value="Pepsin A">Pepsin A</option>
                            <option value="Trypsin + CNBr">Trypsin + CNBr</option>
                            <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
                            <option value="Trypsin, no P rule">Trypsin, no P rule</option>
                            <option value="Whole Protein">Whole Protein</option>
                            <option value="Asp-N">Asp-N</option>
                            <option value="Glu-C">Glu-C</option>
                            <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
                            <option value="Top-Down">Top-Down</option>
                            <option value="Semi-Tryptic">Semi-Tryptic</option>

            <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"/>

                <options from_file="searchgui_mods.loc">
                    <column name="name" index="0" />
                    <column name="value" index="0" />
                </options>
            </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">
                <options from_file="searchgui_mods.loc">
                    <column name="name" index="0" />
                    <column name="value" index="0" />
                </options>