#from datetime import datetime
        #import json
        #import os
        #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 $bin_dir = "bin"

        mkdir output;
        mkdir output_reports;
        mkdir temp_folder;
        mkdir log_folder;
        trap ">&2 cat log_folder/*.log" EXIT;

        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_fasta_file.element_identifier} sequences: ${input_fasta_file.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=4.0.41' >> searchgui.properties;

        #for $peak_list_file in $peak_lists_files:
            #set $input_name = ""
            #if $peak_list_file.is_of_type("mgf"):
                #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf"
            #else if $peak_list_file.is_of_type("mzml"):
                #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mzml", "") + ".mzml"
            #end if
            ln -s -f '${peak_list_file}' '${input_name}';
            #set $encoded_id = $__app__.security.encode_id($peak_list_file.id)
            echo 'Spectrums:${peak_list_file.element_identifier}(API:${encoded_id})';
        #end for

        ## copy the input .par file to the working folder
        cp '${input_parameters_file}' './SEARCHGUI_IdentificationParameters.par';

        ## copy the input .fasta file to the working folder
        cp '${input_fasta_file}' './input_fasta_file.fasta';


        ################
        ## Search CLI ##
        ################
        echo 'running search gui' &&
        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
            --exec_dir="\$cwd/${bin_dir}"
            -use_log_folder 0
            -spectrum_files \$cwd
            -fasta_file "\$cwd/input_fasta_file.fasta"
            -output_folder \$cwd/output
            -id_params ./SEARCHGUI_IdentificationParameters.par
            -temp_folder \$cwd/temp_folder
            -log \$cwd/log_folder
            -threads "\${GALAXY_SLOTS:-12}"

            #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
                -correct_titles "${searchgui_advanced.correct_titles}"
                $searchgui_advanced.missing_titles
                -mgf_splitting "${searchgui_advanced.mgf_splitting}"
                -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
                -output_gzip "${searchgui_advanced.output_gzip}"
            #end if

            #set $engines_list = str($search_engines_options.engines).split(',')
            #if 'X!Tandem' in $engines_list:
                -xtandem 1
            #else
                -xtandem 0
            #end if

            #if 'MyriMatch' in $engines_list:
                -myrimatch 1
            #else
                -myrimatch 0
            #end if

            #if 'MSGF' in $engines_list:
                -msgf 1
            #else
                -msgf 0
            #end if

            #if 'OMSSA' in $engines_list:
                -omssa 1
            #else
                -omssa 0
            #end if

            #if 'Comet' in $engines_list:
                -comet 1
            #else
                -comet 0
            #end if

            #if 'Tide' in $engines_list:
                -tide 1
            #else
                -tide 0
            #end if

            #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

            #if 'MetaMorpheus' in $engines_list:
                -meta_morpheus 1
            #else
                -meta_morpheus 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

            ## mgf and database in output
            -output_data 1

        &&

        echo '>log_folder:' &&

        ls -l \$cwd/log_folder &&

        mv output/searchgui_out.zip searchgui_out.zip

        &&

        zip -u searchgui_out.zip searchgui.properties