comparison searchgui.xml @ 47:44ca2967218c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064

46:baeced706dbc

    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
	<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
	<requirement type="package" version="3.0">zip</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"

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

        ## echo the search engines to run
        echo "$search_engines_options.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 = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
            ln -s -f '${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 $protein_database_options.create_decoy:
            echo "Creating decoy database.";
            searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${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@

        &&

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

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

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

        <!-- Test that specifying non-default search engines works using modifications -->
        <!--
        <test>

47:44ca2967218c

    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
        <requirement type="package" version="3.0">zip</requirement>
    </requirements>
    <expand macro="stdio" />
    <command use_shared_home="false">
<![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;

        ## echo the search engines to run (single quotes important because X!Tandem)
        echo '$search_engines_options.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 = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
            ln -s -f '${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;

        ###########################################
        ####       Set paths                   ####
        ###########################################
        echo 'Setting paths' &&
        searchgui eu.isas.searchgui.cmd.PathSettingsCLI
            --exec_dir="\$cwd/${bin_dir}" 
            -temp_folder \$cwd 
            -log \$cwd/searchgui.log  2>> $temp_stderr &&

        ###########################################
        ####       Creating decoy database     ####
        ###########################################
        #if $protein_database_options.create_decoy:
            echo 'Creating decoy database.' &&
            searchgui eu.isas.searchgui.cmd.FastaCLI 
                --exec_dir="\$cwd/${bin_dir}" 
                -in input_database.fasta
                -decoy  2>> $temp_stderr &&
            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 ##
        #####################################################
        echo 'setting identification parameters' &&
        (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
            --exec_dir="\$cwd/${bin_dir}"
            -out SEARCHGUI_IdentificationParameters.par

            @GENERAL_PARAMETERS@

        &&

        ################
        ## Search CLI ##
        ################
        echo 'running search gui' &&
        (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
            --exec_dir="\$cwd/${bin_dir}"
            -spectrum_files \$cwd
            -output_folder \$cwd/output
            -id_params SEARCHGUI_IdentificationParameters.par

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

            <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="searchgui_results" 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="min_charge" value="1"/>
            <param name="max_charge" value="3"/>
            <param name="engines" value="MS_Amanda"/>
            <output name="searchgui_results" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
        </test>

        <!-- Test that specifying non-default search engines works using modifications -->
        <!--
        <test>