comparison searchgui.xml @ 30:ad60446b1e93 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c

29:78fad25eff17

    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
        <environment_variable name="LC_ALL" action="set_to">C</environment_variable>        
    </requirements>
    <expand macro="stdio" />
    <command>
<![CDATA[
        #from datetime import datetime
        #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
        #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
        #set $temp_stderr = "searchgui_stderr"

        mkdir output;
        mkdir output_reports;
        cwd=`pwd`;
        export HOME=\$cwd;

        ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
        echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;

        cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin;
        tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`;

        #for $mgf in $peak_lists:
            #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
            ln -s -f '${mgf}' '${input_name}';
        #end for
        ##ln -s "${input_database}" input_database.fasta;
        cp "${input_database}" input_database.fasta;

        ###########################################
        ####       Creating decoy database     ####
        ###########################################
        #if $create_decoy:
            echo "Creating decoy database.";
            java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
            rm input_database.fasta &&
            cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
            ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
        #end if

        #####################################################
        ## generate IdentificationParameters for SearchGUI ##
        #####################################################

        (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI
            -out SEARCHGUI_IdentificationParameters.par

            @GENERAL_PARAMETERS@

            -db input_database.fasta
            $use_gene_mapping

            #if $xtandem.xtandem_advanced == "yes"

                -xtandem_npeaks ${xtandem.xtandem_npeaks}
                -xtandem_min_peaks ${xtandem.xtandem_min_peaks}

                -andromeda_frag_method ${andromeda.andromeda_frag_method}
                -andromeda_max_mods ${andromeda.andromeda_max_mods}
                -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length}
                -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length}
                -andromeda_max_psms ${andromeda.andromeda_max_psms}
            #end if
            *#
 
            #* Not working in tests
            #if $tide.tide_advanced == "yes"

            #if $comet.comet_advanced == "yes"

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


                     #if $comet.comet_spectrum.comet_remove_prec == "1"
                        -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}
                     #end if
                     
                     #if $comet.comet_spectrum.comet_remove_prec == "2"
                        -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}
                     #end if
                     
                    -comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower}
                    -comet_clear_mz_range_upper ${comet.comet_spectrum.comet_clear_mz_range_upper}
                #end if

                    -comet_sparse_matrix ${comet.comet_fragment_ions.comet_sparse_matrix}
                    -comet_theoretical_fragment_ions ${comet.comet_fragment_ions.comet_theoretical_fragment_ions}
                #end if
            #end if

        2> $temp_stderr)
        &&

        ################
        ## Search CLI ##
        ################
        (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI 
            -temp_folder `pwd`
            -spectrum_files \$cwd
            -output_folder \$cwd/output
            -id_params SEARCHGUI_IdentificationParameters.par

            #if 'Andromeda' in $engines_list:
                -andromeda 1
            #else
                -andromeda 0
            #end if

            ## single zip file
            -output_option 0

            help="Selecting this option will help PeptideShaker calculate FDR values" />

        <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
            label="gene mappings will be used and saved along with the project (UniProt databases only)"
            help="This should only be enabled for UniProt databaases" />

        <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 -->
        <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>
            <!-- Not working in tests
            <option value="MyriMatch">MyriMatch</option> 
            <option value="MS_Amanda">MS_Amanda</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>
            -->
            <!-- Windows only
            <option value="Andromeda">Andromeda</option>
            -->
            <validator type="no_options" message="Please select at least one output file" />
        </param>


        <!-- General Parameters -->

            <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
                help="Choose a smaller value if you are running on a machine with limited memory"/>

            <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
                help="Choose a smaller value if you are running on a machine with limited memory"/>
        </when>
        </conditional>


        <!-- X!TANDEM ADVANCED PARAMETERS -->
        <conditional name="xtandem">

                <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
                    label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" /> 
                <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
                    label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> 
                <param name="xtandem_evalue" help="Highest value for recorded peptides"
                    label="X!Tandem: Maximum Valid Expectation Value" type="float" value="100" />
                <param name="xtandem_output_proteins" help="Controls output of protein sequences"
                    label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
                <param name="xtandem_output_sequences" help="Controls output of sequence information"
                    label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
                <param name="xtandem_output_spectra" help="Controls output of spectrum information"

                </param>
                <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
                <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
                <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
                <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
            </when>
        </conditional>
        -->

        <!-- Comet ADVANCED PARAMETERS -->

                    <when value="yes">
                        <param name="comet_min_peaks"  type="integer" value="10"
                            label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
                        <param name="comet_min_peak_int"  type="float" value="0.0"
                            label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
                        <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
                            <option value="0"  selected="True" >off</option>
                            <option value="1">on</option>
                            <option value="2">as expected for ETD/ECD spectra</option>
                        </param>
                        <when value="0" />
                        <when value="1">
                            <param name="comet_remove_prec_tol"  type="float" value="1.5"
                                label="Comet: Remove Precursor Tolerance" />
                        </when>
                        <when value="2">
                            <param name="comet_remove_prec_tol"  type="float" value="1.5"
                                label="Comet: Remove Precursor Tolerance" />
                        </when>
                        <param name="comet_clear_mz_range_lower"  type="float" value="0.0"
                            label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" />
                        <param name="comet_clear_mz_range_upper"  type="float" value="0.0"
                            label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" />    
                    </when>

                            label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />                                
                    </when>
                </conditional>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>

            <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="600" /> 
        </test>

        <!-- Test that search works with MSAmanda -->
        <test>
            <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
            <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
            <param name="precursor_ion_tol" value="100"/>

            <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="600" /> 
        </test>


    </tests>
    <help>
**What it does**

Runs multiple search engines on any number of MGF peak lists using the SearchGUI.

30:ad60446b1e93

    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
    </requirements>
    <expand macro="stdio" />
    <command>
<![CDATA[
        #from datetime import datetime
        #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
        #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
        #set $temp_stderr = "searchgui_stderr"
        #set $bin_dir = "bin"

        mkdir output;
        mkdir output_reports;
        cwd=`pwd`;
        export HOME=\$cwd;

        ## echo the search engines to run
        echo "$engines";
        echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";

        ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
        echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;

        #for $mgf in $peak_lists:
            #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
            ln -s -f '${mgf}' '${input_name}';
            #set $encoded_id = $__app__.security.encode_id($mgf.id)
            echo "Spectrums:${mgf.display_name}(API:${encoded_id}) ";
        #end for
        ##ln -s "${input_database}" input_database.fasta;
        cp "${input_database}" input_database.fasta;

        ###########################################
        ####       Creating decoy database     ####
        ###########################################
        #if $create_decoy:
            echo "Creating decoy database.";
            searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy &&
            rm input_database.fasta &&
            cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
            ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
        #end if

        #####################################################
        ## generate IdentificationParameters for SearchGUI ##
        #####################################################
        (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
            --exec_dir="\$cwd/${bin_dir}"
            -out SEARCHGUI_IdentificationParameters.par

            @GENERAL_PARAMETERS@

            -db input_database.fasta
            #if $use_gene_mapping:
                $use_gene_mapping
                $update_gene_mapping
            #end if

            #if $xtandem.xtandem_advanced == "yes"

                -xtandem_npeaks ${xtandem.xtandem_npeaks}
                -xtandem_min_peaks ${xtandem.xtandem_min_peaks}

                -andromeda_frag_method ${andromeda.andromeda_frag_method}
                -andromeda_max_mods ${andromeda.andromeda_max_mods}
                -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length}
                -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length}
                -andromeda_max_psms ${andromeda.andromeda_max_psms}
                -andromeda_decoy_mode ${andromeda.andromeda_decoy_mode}
            #end if
            *#
 
            #* Not working in tests
            #if $tide.tide_advanced == "yes"

            #if $comet.comet_advanced == "yes"

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

                    -comet_remove_prec ${comet.comet_spectrum.comet_prec.comet_remove_prec}


                     #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
                        -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
                     #end if
                     
                     #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
                        -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
                     #end if
                     
                    -comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower}
                    -comet_clear_mz_range_upper ${comet.comet_spectrum.comet_clear_mz_range_upper}
                #end if

                    -comet_sparse_matrix ${comet.comet_fragment_ions.comet_sparse_matrix}
                    -comet_theoretical_fragment_ions ${comet.comet_fragment_ions.comet_theoretical_fragment_ions}
                #end if
            #end if

            #if $directtag.directtag_advanced == "yes"
                -directag_tic_cutoff ${directtag.directag_tic_cutoff}
                -directag_max_peak_count ${directtag.directag_max_peak_count}
                -directag_intensity_classes ${directtag.directag_intensity_classes}
                -directag_adjust_precursor ${directtag.directag_adjust_precursor}
                -directag_min_adjustment ${directtag.directag_min_adjustment}
                -directag_max_adjustment ${directtag.directag_max_adjustment}
                -directag_adjustment_step ${directtag.directag_adjustment_step}
                -directag_charge_states ${directtag.directag_charge_states}
                #if str($directtag.directag_output_suffix).strip() != '':
                -directag_output_suffix ${directtag.directag_output_suffix}
                #end if
                -directag_ms_charge_state ${directtag.directag_ms_charge_state}
                -directag_duplicate_spectra ${directtag.directag_duplicate_spectra}
                -directag_deisotoping ${directtag.directag_deisotoping}
                -directag_isotope_tolerance ${directtag.directag_isotope_tolerance}
                -directag_complement_tolerance ${directtag.directag_complement_tolerance}
                -directag_tag_length ${directtag.directag_tag_length}
                -directag_max_var_mods ${directtag.directag_max_var_mods}
                -directag_max_tag_count ${directtag.directag_max_tag_count}
                -directag_intensity_weight ${directtag.directag_intensity_weight}
                -directag_fidelity_weight ${directtag.directag_fidelity_weight}
                -directag_complement_weight ${directtag.directag_complement_weight}
            #end if

            #if $novor.novor_advanced == "yes"
                -novor_fragmentation ${novor.novor_fragmentation}
                -novor_mass_analyzer ${novor.novor_mass_analyzer}
            #end if

        2> $temp_stderr)
        &&

        ################
        ## Search CLI ##
        ################
        (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI 
            --exec_dir="\$cwd/${bin_dir}"
            -temp_folder `pwd`
            -spectrum_files \$cwd
            -output_folder \$cwd/output
            -id_params SEARCHGUI_IdentificationParameters.par

            #if 'Andromeda' in $engines_list:
                -andromeda 1
            #else
                -andromeda 0
            #end if

            #if 'Novor' in $engines_list:
                -novor 1
            #else
                -novor 0
            #end if

            #if 'DirecTag' in $engines_list:
                -directag 1
            #else
                -directag 0
            #end if

            ## single zip file
            -output_option 0

            help="Selecting this option will help PeptideShaker calculate FDR values" />

        <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
            label="gene mappings will be used and saved along with the project (UniProt databases only)"
            help="This should only be enabled for UniProt databaases" />
        <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
            label="Update gene mappings automatically from Ensembl (UniProt databases only)"
            help="This should only be enabled for UniProt databaases" />

        <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 -->
        <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>
            <!-- Windows only
            <option value="Andromeda">Andromeda</option>
            -->
            <!-- New with version 3.0
            -->
            <!--working in tests
            -->
            <option value="DirecTag">DirecTag</option>
            <option value="Novor">Novor (Select for non-commercial use only)</option>
            <validator type="no_options" message="Please select at least one output file" />
        </param>


        <!-- General Parameters -->

            <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
                help="Choose a smaller value if you are running on a machine with limited memory"/>

            <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
                help="Choose a smaller value if you are running on a machine with limited memory"/>
            </when>
        </conditional>


        <!-- X!TANDEM ADVANCED PARAMETERS -->
        <conditional name="xtandem">

                <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
                    label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" /> 
                <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
                    label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> 
                <param name="xtandem_evalue" help="Highest value for recorded peptides"
                    label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
                <param name="xtandem_output_proteins" help="Controls output of protein sequences"
                    label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
                <param name="xtandem_output_sequences" help="Controls output of sequence information"
                    label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
                <param name="xtandem_output_spectra" help="Controls output of spectrum information"

                </param>
                <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
                <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
                <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
                <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
                <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
            </when>
        </conditional>
        -->

        <!-- Comet ADVANCED PARAMETERS -->

                    <when value="yes">
                        <param name="comet_min_peaks"  type="integer" value="10"
                            label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
                        <param name="comet_min_peak_int"  type="float" value="0.0"
                            label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
                        <conditional name="comet_prec">
                            <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
                                <option value="0"  selected="True" >off</option>
                                <option value="1">on</option>
                                <option value="2">as expected for ETD/ECD spectra</option>
                            </param>
                            <when value="0" />
                            <when value="1">
                                <param name="comet_remove_prec_tol"  type="float" value="1.5"
                                    label="Comet: Remove Precursor Tolerance" />
                            </when>
                            <when value="2">
                                <param name="comet_remove_prec_tol"  type="float" value="1.5"
                                    label="Comet: Remove Precursor Tolerance" />
                            </when>
                        </conditional>
                        <param name="comet_clear_mz_range_lower"  type="float" value="0.0"
                            label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" />
                        <param name="comet_clear_mz_range_upper"  type="float" value="0.0"
                            label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" />    
                    </when>

                            label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />                                
                    </when>
                </conditional>
            </when>
        </conditional>
        <conditional name="directtag">
            <param name="directtag_advanced" type="select" label="DirectTag Options">
                <option value="yes">Advanced</option>
                <option value="no" selected="True">Default</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/>
                <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/>
                <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/>
                <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/>
                <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/>
                <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/>
                <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/>
                <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/>
                <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/>
                <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/>
                <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/>
                <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping">
                    <option value="0" selected="true">no deisotoping</option>
                    <option value="1">precursor only</option>
                    <option value="2">precursor and candidate</option>
                </param>
                <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/>
                <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/>
                <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/>
                <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/>
                <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/>
                <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/>
                <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/>
                <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/>
            </when>
        </conditional>

        <conditional name="novor">
            <param name="novor_advanced" type="select" label="Novor Options">
                <option value="yes">Advanced</option>
                <option value="no" selected="True">Default</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="novor_fragmentation" type="select" label="Novor fragmentation method">
                    <option value="HCD" selected="True">HCD</option>
                    <option value="CID">CID</option>
                </param>
                <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
                    <option value="FT" selected="True">FT</option>
                    <option value="Trap" >Trap</option>
                    <option value="TOF" >TOF</option>
                </param>
            </when>
        </conditional>

    </inputs>
    <outputs>
        <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>

            <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="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
            <param name="precursor_ion_tol" value="100"/>

            <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**

Runs multiple search engines on any number of MGF peak lists using the SearchGUI.