comparison searchgui.xml @ 44:f35bb9d0c93e draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb

43:7963340ab569

<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.3">
    <description>
        Perform protein identification using various search engines and prepare results for input to Peptide Shaker
    </description>
    <macros>
        <import>macros.xml</import>

                -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms}
                -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode}
            #end if
            *#

            #* Not working in tests
            #if $advanced_options.tide.tide_advanced == "yes"
                -tide_num_ptms ${advanced_options.tide.tide_num_ptms}
                -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type}
                -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length}
                -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length}
                -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass}
                -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass}
                -tide_decoy_format ${advanced_options.tide.tide_decoy_format}
                -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals}

                -tide_output_folder ${advanced_options.tide.tide_output_folder}
                -tide_print_peptides ${advanced_options.tide.tide_print_peptides}
                -tide_verbosity ${advanced_options.tide.tide_verbosity}
                -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic}
                -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term}
                -tide_digestion_type ${advanced_options.tide.tide_digestion_type}
                -tide_compute_sp ${advanced_options.tide.tide_compute_sp}
                -tide_max_psms ${advanced_options.tide.tide_max_psms}
                -tide_compute_p ${advanced_options.tide.tide_compute_p}
                -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz}
                -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}
                -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks}
                -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges}
                -tide_remove_prec ${advanced_options.tide.tide_remove_prec}
                -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol}
                -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator}
                -tide_use_flanking ${advanced_options.tide.tide_use_flanking}
                -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses}
                -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width}
                -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset}
                -tide_concat ${advanced_options.tide.tide_concat}
                -tide_export_text ${advanced_options.tide.tide_export_text}
                -tide_export_sqt ${advanced_options.tide.tide_export_sqt}
                -tide_export_pepxml ${advanced_options.tide.tide_export_pepxml}
                -tide_export_mzid ${advanced_options.tide.tide_export_mzid}
                -tide_export_pin ${advanced_options.tide.tide_export_pin}
                -tide_remove_temp ${advanced_options.tide.tide_remove_temp}
            #end if
            *#

            #if $advanced_options.comet.comet_advanced == "yes"

                #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes"
                    -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks}

        </section>
        <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
            help="Select appropriate MGF dataset(s) from history" />

        <!-- Search Engine Selection -->
        <section name="search_engines_options" expanded="false" title="Search Engine Options">
            <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
                <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
                <option value="X!Tandem" selected="True">X!Tandem</option>

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

                </when>
            </conditional>


            <!-- TIDE ADVANCED PARAMETERS -->
            <!-- Not working in tests
            <conditional name="tide">
                <param name="tide_advanced" type="select" label="TIDE Options">
                    <option value="yes">Advanced</option>
                    <option value="no" selected="True">Default</option>
                </param>
                <when value="no" />
                <when value="yes">
                    <param name="tide_num_ptms" type="integer" value="100"
                        label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
                    <param name="tide_num_ptms_per_type" type="integer" value="2"
                        label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
                    <param name="tide_min_pep_length" type="integer" value="6"
                        label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>

                        <option value="NC" selected="True">NC</option>
                        <option value="non" >none</option>
                    </param>
                    <param name="tide_decoy_seed" type="integer" value="1"
                        label="TIDE: Decoy Seed" help="Set the decoy seed"/>
                    <param name="tide_output_folder" type="text" value="crux-output"
                        label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/>
                    <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
                        label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
                    <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
                        <option value="0" >0</option>
                        <option value="10" >10</option>

                        label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
                    <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
                        label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
                    <param name="tide_min_spectrum_mz" type="float" value="0.0"
                        label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
                    <param name="tide_max_spectrum_mz" type="float" value="100000.0"
                        label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
                    <param name="tide_min_spectrum_peaks" type="integer" value="20"
                        label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
                    <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
                        <option value="1" >1</option>

                        label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
                    <param name="tide_mz_bin_offset" type="float" value="0.0"
                        label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
                    <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
                        label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
                    <param name="tide_export_text" type="boolean" truevalue="1" falsevalue="0" checked="true"
                        label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/>
                    <param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false"
                        label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/>
                    <param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false"
                        label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/>
                    <param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false"
                        label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/>
                    <param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false"
                        label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/>
                    <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">

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>

                -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms}
                -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode}
            #end if
            *#

            #if $advanced_options.tide.tide_advanced == "yes"
                #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
                  -tide_num_ptms ${advanced_options.tide.tide_max_spectrum_mz}
                #end if
                -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type}
                -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length}
                -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length}
                -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass}
                -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass}
                -tide_decoy_format ${advanced_options.tide.tide_decoy_format}
                -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals}
                -tide_print_peptides ${advanced_options.tide.tide_print_peptides}
                -tide_verbosity ${advanced_options.tide.tide_verbosity}
                -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic}
                -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term}
                -tide_digestion_type ${advanced_options.tide.tide_digestion_type}
                -tide_compute_sp ${advanced_options.tide.tide_compute_sp}
                -tide_max_psms ${advanced_options.tide.tide_max_psms}
                -tide_compute_p ${advanced_options.tide.tide_compute_p}
                -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz}
                #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
                  -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}
                #end if
                -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks}
                -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges}
                -tide_remove_prec ${advanced_options.tide.tide_remove_prec}
                -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol}
                -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator}
                -tide_use_flanking ${advanced_options.tide.tide_use_flanking}
                -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses}
                -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width}
                -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset}
                -tide_concat ${advanced_options.tide.tide_concat}

                #set $formats = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"]
                #for $format in $formats:
                    #if str($advanced_options.tide.tide_export).strip() == $format:
                      -$format 1
                    #else:
                      -$format 0
                    #end if

                #end for

                -tide_remove_temp ${advanced_options.tide.tide_remove_temp}

            #end if


            #if $advanced_options.comet.comet_advanced == "yes"

                #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes"
                    -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks}

        </section>
        <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
            help="Select appropriate MGF dataset(s) from history" />

        <!-- Search Engine Selection -->
        <section name="search_engines_options" expanded="true" title="Search Engine Options">
            <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
                <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
                <option value="X!Tandem" selected="True">X!Tandem</option>

                <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>

                </when>
            </conditional>


            <!-- TIDE ADVANCED PARAMETERS -->
            <conditional name="tide">
                <param name="tide_advanced" type="select" label="TIDE Options">
                    <option value="yes">Advanced</option>
                    <option value="no" selected="True">Default</option>
                </param>
                <when value="no" />
                <when value="yes">
                    <param name="tide_num_ptms" type="integer" value="" optional="true"
                        label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
                    <param name="tide_num_ptms_per_type" type="integer" value="2"
                        label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
                    <param name="tide_min_pep_length" type="integer" value="6"
                        label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>

                        <option value="NC" selected="True">NC</option>
                        <option value="non" >none</option>
                    </param>
                    <param name="tide_decoy_seed" type="integer" value="1"
                        label="TIDE: Decoy Seed" help="Set the decoy seed"/>
                    <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
                        label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
                    <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
                        <option value="0" >0</option>
                        <option value="10" >10</option>

                        label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
                    <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
                        label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
                    <param name="tide_min_spectrum_mz" type="float" value="0.0"
                        label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
                    <param name="tide_max_spectrum_mz" type="float" value="" optional="true"
                        label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
                    <param name="tide_min_spectrum_peaks" type="integer" value="20"
                        label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
                    <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
                        <option value="1" >1</option>

                        label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
                    <param name="tide_mz_bin_offset" type="float" value="0.0"
                        label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
                    <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
                        label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>

                    <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">