comparison searchgui.xml @ 32:ff592231f118 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d

31:f3f67aa3123b

<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>

            #if $omssa.omssa_advanced == "yes"
                -omssa_hitlist_length ${omssa.hitlist_length}
                -omssa_remove_prec ${omssa.remove_precursor}
                -omssa_scale_prec ${omssa.scale_precursor}
                -omssa_estimate_charge ${omssa.estimate_charge}

                -omssa_memory ${omssa.omssa_memory}
                ## -omssa_isotopes ${omssa.omssa_isotopes} 
                -omssa_neutron ${omssa.omssa_neutron} 
                -omssa_low_intensity "${omssa.omssa_low_intensity}" 
                -omssa_high_intensity ${omssa.omssa_high_intensity} 
                -omssa_intensity_incr ${omssa.omssa_intensity_incr} 
                -omssa_single_window_wd ${omssa.omssa_single_window_wd} 

                -msgf_instrument ${msgf.msgf_instrument} 
                -msgf_fragmentation ${msgf.msgf_fragmentation}
                -msgf_protocol ${msgf.msgf_protocol} 
                -msgf_num_matches ${msgf.msgf_num_matches} 
                -msgf_additional ${msgf.msgf_additional} 
                -msgf_isotope_low ${msgf.msgf_isotope_low} 
                -msgf_isotope_high ${msgf.msgf_isotope_high} 
            #end if
            
            #* Not working in tests
            #if $ms_amanda.ms_amanda_advanced == "yes"
                 -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy}

            #if $myrimatch.myrimatch_advanced == "yes"
                -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length}
                -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
                -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass}
                -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass}
                -myrimatch_isotope_low ${myrimatch.myrimatch_isotope_low}
                -myrimatch_isotope_high ${myrimatch.myrimatch_isotope_high}
                -myrimatch_num_matches ${myrimatch.myrimatch_num_matches}
                -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms}
                -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation}
                -myrimatch_termini ${myrimatch.myrimatch_termini}
                -myrimatch_plus_three ${myrimatch.myrimatch_plus_three}

                <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
                <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
                
                <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
                    label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
                  <!-- param name="omssa_isotopes" type="integer" value="0" 
                      label="OMSSA: Number of Isotopes" help="Number of isotopes to use (integer), 0 implies monoisotopic (default)" / -->
                   <param name="omssa_neutron" type="float" value="1446.94" 
                       label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
                <param name="omssa_low_intensity" type="float" value="0.0" 
                    label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
                <param name="omssa_high_intensity" type="float" value="0.2" 
                    label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />

                <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" />
                <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
                    <option value="0" selected="True">output basic scores only</option>
                    <option value="1" >output additional features</option>
                </param>
                <param name="msgf_isotope_low" label="MSGF: Lower Isotope Error Range" type="integer" value="0" help="Lower isotope error range" />
                <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" /> 
            </when>
        </conditional>

          <!-- MS-AMANDA ADVANCED PARAMETERS  -->
        <!-- Not working in tests

                    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_isotope_low"  type="integer" value="-1"
                    label="MyriMatch: Lower Isotope Error Range" help="Lower isotope error ragne" />
                <param name="myrimatch_isotope_high"  type="integer" value="2"
                    label="MyriMatch: Upper Isotope Error Range" help="Upper isotope error range" />
                <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*)">

            <param name="min_charge" value="1"/>
            <param name="max_charge" value="3"/>
            <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
            <param name="xtandem.xtandem_advanced" value="yes"/>
            <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>

            <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> 
        </test>
        <!-- Test that search works with MSAmanda -->
        <test>
            <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>

            <param name="fixed_modifications" value="carbamidomethyl c"/>
            <param name="variable_modifications" value="oxidation of m"/>
            <param name="min_charge" value="1"/>
            <param name="max_charge" value="3"/>
            <param name="engines" value="MS_Amanda"/>

            <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> 
        </test>
    </tests>
    <help>
**What it does**

32:ff592231f118

<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">
    <description>
        Perform protein identification using various search engines and prepare results for input to Peptide Shaker
    </description>
    <macros>
        <import>macros.xml</import>

            #if $omssa.omssa_advanced == "yes"
                -omssa_hitlist_length ${omssa.hitlist_length}
                -omssa_remove_prec ${omssa.remove_precursor}
                -omssa_scale_prec ${omssa.scale_precursor}
                -omssa_estimate_charge ${omssa.estimate_charge}
                -omssa_memory ${omssa.omssa_memory}
                -omssa_neutron ${omssa.omssa_neutron} 
                -omssa_low_intensity "${omssa.omssa_low_intensity}" 
                -omssa_high_intensity ${omssa.omssa_high_intensity} 
                -omssa_intensity_incr ${omssa.omssa_intensity_incr} 
                -omssa_single_window_wd ${omssa.omssa_single_window_wd} 

                -msgf_instrument ${msgf.msgf_instrument} 
                -msgf_fragmentation ${msgf.msgf_fragmentation}
                -msgf_protocol ${msgf.msgf_protocol} 
                -msgf_num_matches ${msgf.msgf_num_matches} 
                -msgf_additional ${msgf.msgf_additional} 
            #end if
            
            #* Not working in tests
            #if $ms_amanda.ms_amanda_advanced == "yes"
                 -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy}

            #if $myrimatch.myrimatch_advanced == "yes"
                -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length}
                -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
                -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass}
                -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass}
                -myrimatch_num_matches ${myrimatch.myrimatch_num_matches}
                -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms}
                -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation}
                -myrimatch_termini ${myrimatch.myrimatch_termini}
                -myrimatch_plus_three ${myrimatch.myrimatch_plus_three}

                <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
                <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
                
                <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
                    label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
                <param name="omssa_neutron" type="float" value="1446.94" 
                       label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
                <param name="omssa_low_intensity" type="float" value="0.0" 
                    label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
                <param name="omssa_high_intensity" type="float" value="0.2" 
                    label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />

                <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" />
                <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
                    <option value="0" selected="True">output basic scores only</option>
                    <option value="1" >output additional features</option>
                </param>
            </when>
        </conditional>

          <!-- MS-AMANDA ADVANCED PARAMETERS  -->
        <!-- Not working in tests

                    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*)">

            <param name="min_charge" value="1"/>
            <param name="max_charge" value="3"/>
            <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
            <param name="xtandem.xtandem_advanced" value="yes"/>
            <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
            <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> 
        </test>
        <!-- Test that search works with MSAmanda -->
        <test>
            <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>

            <param name="fixed_modifications" value="carbamidomethyl c"/>
            <param name="variable_modifications" value="oxidation of m"/>
            <param name="min_charge" value="1"/>
            <param name="max_charge" value="3"/>
            <param name="engines" value="MS_Amanda"/>
            <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> 
        </test>
    </tests>
    <help>
**What it does**