comparison searchgui.xml @ 45:5fa8b409599e draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544

44:f35bb9d0c93e

<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.4">
    <description>
        Perform protein identification using various search engines and prepare results for input to Peptide Shaker
    </description>
    <macros>
        <import>macros.xml</import>

                 -ms_amanda_instrument "${advanced_options.ms_amanda.ms_amanda_instrument}"
                 -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank}
                 -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono}
            #end if

            #* Not working in tests
            #if $advanced_options.myrimatch.myrimatch_advanced == "yes"
                -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}
                -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}
                -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass}
                -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass}

                -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes}
                -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier}
                -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches}
                -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}
            #end if
            *#

            #* Not working in tests
            #if $advanced_options.andromeda.andromeda_advanced == "yes"
                -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass}
                -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb}

                <option value="MSGF" selected="True">MS-GF+</option>
                <option value="OMSSA" selected="True">OMSSA</option>
                <option value="Comet">Comet</option>
                <option value="Tide">Tide</option>
                <!-- Not working in tests
                -->
                <option value="MyriMatch">MyriMatch</option>
                <option value="MS_Amanda">MS_Amanda</option>
                <!-- Windows only
                <option value="Andromeda">Andromeda</option>
                -->

                    <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format">
                        <option value="tide_export_text" selected="True">Text</option>
                        <option value="tide_export_sqt" >SQT</option>
                        <option value="tide_export_pepxml" >pepxml</option>
              <!--
                        MZidentML and Percolator input file options generates files with the format (ie. if we use a spectrum file called ´qExactive01819´):
                        galaxy/database/jobs_directory/000/88/working/bin/resources/Tide/linux/linux_64bit/crux-output/qExactive01819.tide-search.target.mzid
                        instead of
                        galaxy/database/jobs_directory/000/88/working/bin/resources/Tide/linux/linux_64bit/crux-output/qExactive01819.tide-search.mzid
                        which is the expected one, so current searchgui version gives a "does not exist error".
              -->
              <!--
                        <option value="tide_export_mzid" >MzIdentML</option
                        <option value="tide_export_pin" >Percolator input file</option>
              -->
                    </param>

                    <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
                        label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
                </when>
            </conditional>


            <!-- MyriMatch ADVANCED PARAMETERS -->
            <!-- Not working in tests
            <conditional name="myrimatch">
                <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
                    <option value="yes">Advanced</option>
                    <option value="no" selected="True">Default</option>
                </param>
                <when value="no" />
                <when value="yes">
                    <param name="myrimatch_min_pep_length"  type="integer" value="6"
                        label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
                    <param name="myrimatch_max_pep_length"  type="integer" value="30"
                        label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
                    <param name="myrimatch_min_prec_mass"  type="float" value="0.0"
                        label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" />
                    <param name="myrimatch_max_prec_mass"  type="float" value="10000.0"
                        label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" />
                    <param name="myrimatch_num_matches"  type="integer" value="10"
                        label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
                    <param name="myrimatch_num_ptms"  type="integer" value="2"
                        label="MyriMatch: Number of PTMs" help="Set the number of PTMS allowed per peptide" />
                    <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
                        <option value="CID" selected="True">CID</option>
                        <option value="ETD" >ETD</option>
                    </param>
                    <param name="myrimatch_termini" label="MyriMatch: Number of Enzymatic Termini" type="select" help="Select the number of enzymatic termini">
                        <option value="0">non-tryptic</option>
                        <option value="1" >semi-tryptic</option>
                        <option value="2"  selected="True" >fully-tryptic</option>
                    </param>
                    <param name="myrimatch_plus_three"  type="boolean" truevalue="1" falsevalue="0" checked="true"
                        label="MyriMatch: Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
                    <param name="myrimatch_xcorr"  type="boolean" truevalue="1" falsevalue="0" checked="false"
                        label="MyriMatch: Xcorr Option" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
                    <param name="myrimatch_tic_cutoff"  type="float" value="0.98"
                        label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained" />
                    <param name="myrimatch_intensity_classes"  type="integer" value="3"
                        label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
                    <param name="myrimatch_class_multiplier"  type="integer" value="2"
                        label="MyriMatch: Class Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />
                    <param name="myrimatch_num_batches"  type="integer" value="50"
                        label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
                    <param name="myrimatch_max_peak"  type="integer" value="100"
                        label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
                </when>
            </conditional>
            -->

            <!-- Andromeda ADVANCED PARAMETERS -->
            <!-- Windows only
            <conditional name="andromeda">
                <param name="andromeda_advanced" type="select" label="Andromeda Options">

45:5fa8b409599e

<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">
    <description>
        Perform protein identification using various search engines and prepare results for input to Peptide Shaker
    </description>
    <macros>
        <import>macros.xml</import>

                 -ms_amanda_instrument "${advanced_options.ms_amanda.ms_amanda_instrument}"
                 -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank}
                 -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono}
            #end if

            #if $advanced_options.myrimatch.myrimatch_advanced == "yes"
                -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}
                -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}
                -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass}
                -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass}

                -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes}
                -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier}
                -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches}
                -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}
            #end if


            #* Not working in tests
            #if $advanced_options.andromeda.andromeda_advanced == "yes"
                -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass}
                -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb}

                <option value="MSGF" selected="True">MS-GF+</option>
                <option value="OMSSA" selected="True">OMSSA</option>
                <option value="Comet">Comet</option>
                <option value="Tide">Tide</option>
                <option value="MyriMatch">MyriMatch</option>
                <option value="MS_Amanda">MS_Amanda</option>
                <!-- Windows only
                <option value="Andromeda">Andromeda</option>
                -->

                    <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format">
                        <option value="tide_export_text" selected="True">Text</option>
                        <option value="tide_export_sqt" >SQT</option>
                        <option value="tide_export_pepxml" >pepxml</option>
                        <option value="tide_export_mzid" >MzIdentML</option>
                        <option value="tide_export_pin" >Percolator input file</option>
                    </param>

                    <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
                        label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
                </when>
            </conditional>


            <!-- MyriMatch ADVANCED PARAMETERS -->
            <conditional name="myrimatch">
                <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
                    <option value="yes">Advanced</option>
                    <option value="no" selected="True">Default</option>
                </param>
                <when value="no" />
                <when value="yes">
                    <param name="myrimatch_min_pep_length"  type="integer" value="8"
                        label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
                    <param name="myrimatch_max_pep_length"  type="integer" value="30"
                        label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
                    <param name="myrimatch_min_prec_mass"  type="float" value="600.0"
                        label="MyriMatch: Minimum Precursor Mass" help="Minimum precursor mass of parent ion to be considered" />
                    <param name="myrimatch_max_prec_mass"  type="float" value="5000.0"
                        label="MyriMatch: Maximum Precursor Mass" help="Maximum precursor mass of parent ion to be considered" />
                    <param name="myrimatch_num_matches"  type="integer" value="10"
                        label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
                    <param name="myrimatch_num_ptms"  type="integer" value="2"
                        label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" />
                    <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
                        <option value="CID" selected="True">CID</option>
                        <option value="HCD" >HCD</option>
                        <option value="ETD" >ETD</option>
                    </param>
                    <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals">
                        <option value="0">None required</option>
                        <option value="1">At least one</option>
                        <option value="2" selected="True" >Both</option>
                    </param>
                    <param name="myrimatch_plus_three"  type="boolean" truevalue="1" falsevalue="0" checked="true"
                        label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
                    <param name="myrimatch_xcorr"  type="boolean" truevalue="1" falsevalue="0" checked="false"
                        label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
                    <param name="myrimatch_tic_cutoff"  type="float" value="0.98"
                        label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained (0.0 - 1.0)" />
                    <param name="myrimatch_intensity_classes"  type="integer" value="3"
                        label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
                    <param name="myrimatch_class_multiplier"  type="integer" value="2"
                        label="MyriMatch: Class Size Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />
                    <param name="myrimatch_num_batches"  type="integer" value="50"
                        label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
                    <param name="myrimatch_max_peak"  type="integer" value="100"
                        label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
                </when>
            </conditional>


            <!-- Andromeda ADVANCED PARAMETERS -->
            <!-- Windows only
            <conditional name="andromeda">
                <param name="andromeda_advanced" type="select" label="Andromeda Options">