comparison searchgui.xml @ 15:3fa49ed11f3d draft

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14:0c50fe88ebfc

        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\#\#/*/}"`;

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

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

            @GENERAL_PARAMETERS@

            -db input_database.fasta

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

            #if $tide.tide_advanced == "yes"
                -tide_num_ptms ${tide.tide_num_ptms}
                -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type}
                -tide_min_pep_length ${tide.tide_min_pep_length}

        ################
        (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.parameters

            -threads "\${GALAXY_SLOTS:-12}"

            #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
                -correct_titles "${searchgui_advanced.correct_titles}"

            #if 'MS_Amanda' in $engines_list:
                -ms_amanda 1
            #else
                -ms_amanda 0
            #end if

            ## single zip file
            -output_option 0

            <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>
            <option value="Tide">Tide</option>
            <validator type="no_options" message="Please select at least one output file" />
        </param>


        <!-- General Parameters -->

                    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>

        <!-- Comet ADVANCED PARAMETERS -->
        <conditional name="comet">
            <param name="comet_advanced" type="select" label="Comet Options">
                <option value="yes">Advanced</option>

15:3fa49ed11f3d

        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\#\#/*/}"`;

        #####################################################
        ## 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

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

            #*
            #if $andromeda.andromeda_advanced == "yes"
                -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass}
                -andromeda_max_comb ${andromeda.andromeda_max_comb}
                -andromeda_top_peaks ${andromeda.andromeda_top_peaks}
                -andromeda_top_peaks_window ${andromeda.andromeda_top_peaks_window}
                -andromeda_incl_water ${andromeda.andromeda_incl_water}
                -andromeda_incl_ammonia ${andromeda.andromeda_incl_ammonia}
                -andromeda_neutral_losses ${andromeda.andromeda_neutral_losses}
                -andromeda_fragment_all ${andromeda.andromeda_fragment_all}
                -andromeda_emp_correction ${andromeda.andromeda_emp_correction}
                -andromeda_higher_charge ${andromeda.andromeda_higher_charge}
                -andromeda_equal_il ${andromeda.andromeda_equal_il}
                -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
            *#

            #if $tide.tide_advanced == "yes"
                -tide_num_ptms ${tide.tide_num_ptms}
                -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type}
                -tide_min_pep_length ${tide.tide_min_pep_length}

        ################
        (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

            -threads "\${GALAXY_SLOTS:-12}"

            #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
                -correct_titles "${searchgui_advanced.correct_titles}"

            #if 'MS_Amanda' in $engines_list:
                -ms_amanda 1
            #else
                -ms_amanda 0
            #end if

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

            ## single zip file
            -output_option 0

            <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>
            <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 -->

                    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">
                <option value="yes">Advanced</option>
                <option value="no" selected="True">Default</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" />
                <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" />
                <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" />
                <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" />
                <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" />
                <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" />
                <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" />
                <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" />
                <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" />
                <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" />
                <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" />
                <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." >
                   <option value="CID" selected="true">CID</option>
                   <option value="HCD">HCD</option>
                   <option value="EDT">EDT</option>
                </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 -->
        <conditional name="comet">
            <param name="comet_advanced" type="select" label="Comet Options">
                <option value="yes">Advanced</option>