view peptide_shaker.xml @ 5:4b15d68afa6c draft

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<tool id="peptide_shaker" name="Peptide Shaker" version="1.18.3.0">
    <description>
        Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
    </description>
    <requirements>
        <requirement type="package" version="0.28.0">peptide_shaker</requirement>
        <requirement type="package" version="1.18.0">searchgui</requirement>
        <requirement type="package" version="2.2.29">blast+</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Job Failed" />
    </stdio>
    <command>
        #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")
        mkdir output;
        mkdir output_reports;
        cwd=`pwd`;
        #for $mgf in $peak_lists:
            #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
            ln -s '${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 \$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 \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI
            -out SEARCHGUI_IdentificationParameters.parameters
            -prec_ppm "${precursor_ion_tol_units}"
            -prec_tol "${precursor_ion_tol}"
            -frag_tol "${fragment_tol}"
            -enzyme "${enzyme}"
            #set $fixed_mods_str = $fixed_modifications or ''
            #set $variable_mods_str = $variable_modifications or ''
            #if $fixed_mods_str
                -fixed_mods "${fixed_mods_str}" 
            #end if
            #if $variable_mods_str
                -variable_mods "${variable_mods_str}"
            #end if
            -min_charge "${min_charge}"
            -max_charge "${max_charge}"
            -mc "${missed_cleavages}"
            -fi "${forward_ion}"
            -ri "${reverse_ion}"
            -db input_database.fasta

            #if $advanced.advanced_type_selector == "advanced":

                ##if $advanced.xtandem.xtandem_selector == "yes"
                ##end if

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

                ##if $advanced.msgf.msgf_selector == "yes"
                ##end if

                ##if $advanced.ms_amanda.ms_amanda_selector == "yes"
                ##end if

            #end if
        ;

        ################
        ## Search CLI ##
        ################
        java -cp \$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}"
            -correct_titles "${correct_titles}"
            -mgf_splitting "${mgf_splitting}"
            -mgf_spectrum_count "${mgf_spectrum_count}"

            ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
            ## the tree is generated afterwards in PeptideShaker
            -protein_tree 0

            -makeblastdb_folder \$BLAST_ROOT_DIR

            #if $advanced.advanced_type_selector == "advanced":

                #if $advanced.xtandem.xtandem_selector == "yes"
                    -xtandem 1
                #else
                    -xtandem 0
                #end if

                #if $advanced.omssa.omssa_selector == "yes"
                    -omssa 1
                #else
                    -omssa 0
                #end if

                #if $advanced.msgf.msgf_selector == "yes"
                    -msgf 1
                #else
                    -msgf 0
                #end if

                #if $advanced.ms_amanda.ms_amanda_selector == "yes"
                    -ms_amanda 1
                #else
                    -ms_amanda 0
                #end if

            #end if
        ;

        #########################################################
        ## generate IdentificationParameters for PeptideShaker ##
        #########################################################
        java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI
            -out PEPTIDESHAKER_IdentificationParameters.parameters
            -prec_ppm "${precursor_ion_tol_units}"
            -prec_tol "${precursor_ion_tol}"
            -frag_tol "${fragment_tol}"
            -enzyme "${enzyme}"
            #set $fixed_mods_str = $fixed_modifications or ''
            #set $variable_mods_str = $variable_modifications or ''
            #if $fixed_mods_str
                -fixed_mods "$fixed_mods_str" 
            #end if
            #if $variable_mods_str
                -variable_mods "$variable_mods_str"
            #end if
            -min_charge $min_charge
            -max_charge $max_charge
            -mc $missed_cleavages
            -fi $forward_ion
            -ri $reverse_ion
            -db input_database.fasta
        ;

        ######################
        ## PeptideShakerCLI ##
        ######################
        java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI
            -temp_folder `pwd`
            -experiment '${exp_str}'
            -sample '${samp_str}'
            -replicate 1
            -spectrum_files \$cwd
            -identification_files \$cwd/output
            -out \$cwd/peptide_shaker_output.cps
            -id_params PEPTIDESHAKER_IdentificationParameters.parameters

            ##Optional gene annotation parameter
            #if $species_type.species_type_selector != 'no_species_type':
                -species_type "${species_type.species_type_selector}"
                -species "${species_type.species}"
            #end if

            ##Optional processing parameters:
            #if $processing_options.processing_options_selector == "yes"
                -protein_FDR "${processing_options.protein_fdr}"
                -peptide_FDR "${processing_options.peptide_fdr}"
                -psm_FDR "${processing_options.psm_fdr}"
                -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
                #if $processing_options.ptm_score.ptm_score_selector == 1
                    -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
                    #if str($processing_options.ptm_score.ptm_threshold) != ''
                        -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
                    #end if
                #end if
                -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
            #end if

           ##Optional filtering parameters:
            #if $filtering_options.filtering_options_selector == "yes":
                -min_peptide_length "${filtering_options.min_peptide_length}"
                -max_peptide_length "${filtering_options.max_peptide_length}"
                -max_precursor_error "${filtering_options.max_precursor_error}"
                -max_precursor_error_type "${filtering_options.max_precursor_error_type}"
                -max_xtandem_e "${filtering_options.max_xtandem_e}"
                -max_omssa_e "${filtering_options.max_omssa_e}"
                -max_mascot_e "${filtering_options.max_mascot_e}"
                -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
            #end if
        ;

        ##################################
        ## PeptideShaker Report options ##
        ##################################
        java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI
            -temp_folder `pwd`
            -in \$cwd/peptide_shaker_output.cps
            -out_reports \$cwd/output_reports
            #if 'cps' in str($outputs).split(','):
                #set $cleaned_list = str($outputs).split(',')
                #silent $cleaned_list.remove('cps')
                -reports #echo ','.join($cleaned_list)#
            #else:
                -reports #echo str($outputs)#
            #end if
        ;

        rm /home/bag/test/foo/* -rf ;
        cp -R \$cwd /home/bag/test/foo/ ;

        #if '0' in str($outputs).split(','):
            find \$cwd/output_reports -name '*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
            ;
        #end if
        #if '2' in str($outputs).split(','):
            find \$cwd/output_reports -name '*PSM*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
            ;
        #end if
        #if '3' in str($outputs).split(','):
            find \$cwd/output_reports -name '*Peptide*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
            ;
        #end if
        #if '4' in str($outputs).split(','):
            find \$cwd/output_reports -name '*Protein*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
            ;
        #end if
        #if '1' in str($outputs).split(','):
            find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
            ;
        #end if

        ##cd ..;
        ## the following line is needed. Otherwise, Galaxy will strip away the ';'
        echo 'Finished!';
    </command>
    <inputs>
        <param format="fasta" name="input_database" type="data" label="Protein Database"
            help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/>

        <param name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" />

        <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)"
            help="Select appropriate MGF dataset(s) from history" />
        <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
            help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
            <option value="1">Parts per million (ppm)</option>
            <option value="0">Daltons</option>
        </param>
        <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"
            help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
        <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"
            help="Provide error value for fragment ions, based on instrument used"/>
        <param name="enzyme" type="select" label="Enzyme"
            help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
            <option value="Trypsin">Trypsin</option>
            <option value="Arg-C">Arg-C</option>
            <option value="CNBr">CNBr</option>
            <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
            <option value="Formic Acid">Formic Acid</option>
            <option value="Lys-C">Lys-C</option>
            <option value="Lys-C, no P rule">Lys-C, no P rule</option>
            <option value="Pepsin A">Pepsin A</option>
            <option value="Trypsin + CNBr">Trypsin + CNBr</option>
            <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
            <option value="Trypsin, no P rule">Trypsin, no P rule</option>
            <option value="whole protein">whole protein</option>
            <option value="Asp-N">Asp-N</option>
            <option value="Glu-C">Glu-C</option>
            <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
            <option value="Top-Down">Top-Down</option>
            <option value="Semi-Tryptic">Semi-Tryptic</option>
            <option value="No enzyme">No enzyme</option>
            <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
            <option value="Asp-N (DE)">Asp-N (DE)</option>
            <option value="Glu-C (DE)">Glu-C (DE)</option>
            <option value="Lys-N (K)">Lys-N (K)</option>
            <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
            <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
            <option value="Semi-Glu-C">Semi-Glu-C</option>
        </param>

        <param name="correct_titles" type="select" label="Correct for duplicate spectrum titles"
            help="(-correct_titles)">
            <option value="0">no correction</option>
            <option value="1" selected="True">rename spectra</option>
            <option value="2">delete spectra</option>
        </param>

        <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
            help="(-mgf_splitting)"/>
        <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
            help="(-mgf_spectrum_count)"/>

        <conditional name="species_type">
            <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
                help="(-species_type)">
                <option value="Fungi">Fungi</option>
                <option value="Plants">Plants</option>
                <option value="Metazoa">Metazoa</option>
                <option value="Vertebrates">Vertebrates</option>
                <option value="Protists">Protists</option>
                <option value="no_species_type" selected="true">No species restriction</option>
            </param>
            <when value="Protists">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="(-species)">
                    <option value="Albugo laibachii">Albugo laibachii</option>
                    <option value="Dictyostelium discoideum">Dictyostelium discoideum</option>
                    <option value="Entamoeba histolytica">Entamoeba histolytica</option>
                    <option value="Giardia lamblia">Giardia lamblia</option>
                    <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option>
                    <option value="Hyaloperonospora arabidopsidis">Hyaloperonospora arabidopsidis</option>
                    <option value="Leishmania major">Leishmania major</option>
                    <option value="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option>
                    <option value="Phytophthora infestans">Phytophthora infestans</option>
                    <option value="Phytophthora ramorum">Phytophthora ramorum</option>
                    <option value="Phytophthora sojae">Phytophthora sojae</option>
                    <option value="Plasmodium berghei">Plasmodium berghei</option>
                    <option value="Plasmodium chabaudi">Plasmodium chabaudi</option>
                    <option value="Plasmodium falciparum">Plasmodium falciparum</option>
                    <option value="Plasmodium knowlesi">Plasmodium knowlesi</option>
                    <option value="Plasmodium vivax">Plasmodium vivax</option>
                    <option value="Pythium ultimum">Pythium ultimum</option>
                    <option value="Tetrahymena thermophila">Tetrahymena thermophila</option>
                    <option value="Thalassiosira pseudonana">Thalassiosira pseudonana</option>
                    <option value="Toxoplasma gondii">Toxoplasma gondii</option>
                    <option value="Trypanosoma brucei">Trypanosoma brucei</option>
                </param>
            </when>
            <when value="Plants">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="(-species)">
                    <option value="Arabidopsis lyrata">Arabidopsis lyrata</option>
                    <option value="Arabidopsis thaliana">Arabidopsis thaliana</option>
                    <option value="Brachypodium distachyon">Brachypodium distachyon</option>
                    <option value="Brassica rapa genes">Brassica rapa genes</option>
                    <option value="Chlamydomonas reinhardtii">Chlamydomonas reinhardtii</option>
                    <option value="Cyanidioschyzon merolae">Cyanidioschyzon merolae</option>
                    <option value="Glycine max">Glycine max</option>
                    <option value="Hordeum vulgare">Hordeum vulgare</option>
                    <option value="Medicago truncatula">Medicago truncatula</option>
                    <option value="Musa acuminata">Musa acuminata</option>
                    <option value="Oryza brachyantha">Oryza brachyantha</option>
                    <option value="Oryza glaberrima">Oryza glaberrima</option>
                    <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option>
                    <option value="Oryza sativa">Oryza sativa</option>
                    <option value="Physcomitrella patens">Physcomitrella patens</option>
                    <option value="Populus trichocarpa">Populus trichocarpa</option>
                    <option value="Selaginella moellendorffii">Selaginella moellendorffii</option>
                    <option value="Setaria italica">Setaria italica</option>
                    <option value="Solanum lycopersicum">Solanum lycopersicum</option>
                    <option value="Solanum tuberosum">Solanum tuberosum</option>
                    <option value="Sorghum bicolor">Sorghum bicolor</option>
                    <option value="Vitis vinifera">Vitis vinifera</option>
                    <option value="Zea mays">Zea mays</option>
                </param>
            </when>
            <when value="Metazoa">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="(-species)">
                    <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option>
                    <option value="Aedes aegypti">Aedes aegypti</option>
                    <option value="Amphimedon queenslandica">Amphimedon queenslandica</option>
                    <option value="Anopheles darlingi">Anopheles darlingi</option>
                    <option value="Anopheles gambiae">Anopheles gambiae</option>
                    <option value="Apis mellifera">Apis mellifera</option>
                    <option value="Atta cephalotes">Atta cephalotes</option>
                    <option value="Bombyx mori">Bombyx mori</option>
                    <option value="Brugia malayi">Brugia malayi</option>
                    <option value="Caenorhabditis brenneri">Caenorhabditis brenneri</option>
                    <option value="Caenorhabditis briggsae">Caenorhabditis briggsae</option>
                    <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
                    <option value="Caenorhabditis japonica">Caenorhabditis japonica</option>
                    <option value="Caenorhabditis remanei">Caenorhabditis remanei</option>
                    <option value="Culex quinquefasciatus">Culex quinquefasciatus</option>
                    <option value="Danaus plexippus">Danaus plexippus</option>
                    <option value="Daphnia pulex">Daphnia pulex</option>
                    <option value="Drosophila ananassae">Drosophila ananassae</option>
                    <option value="Drosophila erecta">Drosophila erecta</option>
                    <option value="Drosophila grimshawi">Drosophila grimshawi</option>
                    <option value="Drosophila melanogaster">Drosophila melanogaster</option>
                    <option value="Drosophila mojavensis">Drosophila mojavensis</option>
                    <option value="Drosophila persimilis">Drosophila persimilis</option>
                    <option value="Drosophila pseudoobscura">Drosophila pseudoobscura</option>
                    <option value="Drosophila sechellia">Drosophila sechellia</option>
                    <option value="Drosophila simulans">Drosophila simulans</option>
                    <option value="Drosophila virilis">Drosophila virilis</option>
                    <option value="Drosophila willistoni">Drosophila willistoni</option>
                    <option value="Drosophila yakuba">Drosophila yakuba</option>
                    <option value="Heliconius melpomene">Heliconius melpomene</option>
                    <option value="Ixodes scapularis">Ixodes scapularis</option>
                    <option value="Loa loa">Loa loa</option>
                    <option value="Megaselia scalaris">Megaselia scalaris</option>
                    <option value="Nasonia vitripennis">Nasonia vitripennis</option>
                    <option value="Nematostella vectensis">Nematostella vectensis</option>
                    <option value="Pediculus humanus">Pediculus humanus</option>
                    <option value="Pristionchus pacificus">Pristionchus pacificus</option>
                    <option value="Schistosoma mansoni">Schistosoma mansoni</option>
                    <option value="Strigamia maritima">Strigamia maritima</option>
                    <option value="Strongylocentrotus purpuratus">Strongylocentrotus purpuratus</option>
                    <option value="Tribolium castaneum">Tribolium castaneum</option>
                    <option value="Trichinella spiralis">Trichinella spiralis</option>
                    <option value="Trichoplax adhaerens">Trichoplax adhaerens</option>
                </param>
            </when>
            <when value="Fungi">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="(-species)">
                    <option value="Ashbya gossypii">Ashbya gossypii</option>
                    <option value="Aspergillus clavatus">Aspergillus clavatus</option>
                    <option value="Aspergillus flavus">Aspergillus flavus</option>
                    <option value="Aspergillus fumigatus">Aspergillus fumigatus</option>
                    <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option>
                    <option value="Aspergillus nidulans">Aspergillus nidulans</option>
                    <option value="Aspergillus niger">Aspergillus niger</option>
                    <option value="Aspergillus oryzae">Aspergillus oryzae</option>
                    <option value="Aspergillus terreus">Aspergillus terreus</option>
                    <option value="Botryotinia fuckeliana">Botryotinia fuckeliana</option>
                    <option value="Cryptococcus neoformans">Cryptococcus neoformans</option>
                    <option value="Fusarium oxysporum">Fusarium oxysporum</option>
                    <option value="Gaeumannomyces graminis">Gaeumannomyces graminis</option>
                    <option value="Gibberella moniliformis">Gibberella moniliformis</option>
                    <option value="Gibberella zeae">Gibberella zeae</option>
                    <option value="Glomerella graminicola">Glomerella graminicola</option>
                    <option value="Komagataella pastoris">Komagataella pastoris</option>
                    <option value="Leptosphaeria maculans">Leptosphaeria maculans</option>
                    <option value="Magnaporthe oryzae">Magnaporthe oryzae</option>
                    <option value="Magnaporthe poae">Magnaporthe poae</option>
                    <option value="Melampsora larici-populina">Melampsora larici-populina</option>
                    <option value="Nectria haematococca">Nectria haematococca</option>
                    <option value="Neosartorya fischeri">Neosartorya fischeri</option>
                    <option value="Neurospora crassa">Neurospora crassa</option>
                    <option value="Phaeosphaeria nodorum">Phaeosphaeria nodorum</option>
                    <option value="Puccinia graminis">Puccinia graminis</option>
                    <option value="Puccinia triticina">Puccinia triticina</option>
                    <option value="Pyrenophora teres">Pyrenophora teres</option>
                    <option value="Pyrenophora tritici-repentis">Pyrenophora tritici-repentis</option>
                    <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option>
                    <option value="Schizosaccharomyces pombe">Schizosaccharomyces pombe</option>
                    <option value="Sclerotinia sclerotiorum">Sclerotinia sclerotiorum</option>
                    <option value="Sporisorium reilianum">Sporisorium reilianum</option>
                    <option value="Trichoderma reesei">Trichoderma reesei</option>
                    <option value="Trichoderma virens">Trichoderma virens</option>
                    <option value="Tuber melanosporum">Tuber melanosporum</option>
                    <option value="Ustilago maydis">Ustilago maydis</option>
                    <option value="Yarrowia lipolytica">Yarrowia lipolytica</option>
                    <option value="Zymoseptoria tritici">Zymoseptoria tritici</option>
                </param>
            </when>
            <when value="Vertebrates">
                <param name="species" type="select" label="The species to use for the gene annotation"
                    help="(-species)">
                    <option value="Ailuropoda melanoleuca">Ailuropoda melanoleuca</option>
                    <option value="Anolis carolinensis">Anolis carolinensis</option>
                    <option value="Bos taurus">Bos taurus</option>
                    <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
                    <option value="Callithrix jacchus">Callithrix jacchus</option>
                    <option value="Canis familiaris">Canis familiaris</option>
                    <option value="Cavia porcellus">Cavia porcellus</option>
                    <option value="Choloepus hoffmanni">Choloepus hoffmanni</option>
                    <option value="Ciona intestinalis">Ciona intestinalis</option>
                    <option value="Ciona savignyi">Ciona savignyi</option>
                    <option value="Danio rerio">Danio rerio</option>
                    <option value="Dasypus novemcinctus">Dasypus novemcinctus</option>
                    <option value="Dipodomys ordii">Dipodomys ordii</option>
                    <option value="Drosophila melanogaster">Drosophila melanogaster</option>
                    <option value="Echinops telfairi">Echinops telfairi</option>
                    <option value="Equus caballus">Equus caballus</option>
                    <option value="Erinaceus europaeus">Erinaceus europaeus</option>
                    <option value="Felis catus">Felis catus</option>
                    <option value="Gallus gallus">Gallus gallus</option>
                    <option value="Gasterosteus aculeatus">Gasterosteus aculeatus</option>
                    <option value="Gorilla gorilla">Gorilla gorilla</option>
                    <option value="Homo sapiens">Homo sapiens</option>
                    <option value="Ictidomys tridecemlineatus">Ictidomys tridecemlineatus</option>
                    <option value="Latimeria chalumnae">Latimeria chalumnae</option>
                    <option value="Loxodonta africana">Loxodonta africana</option>
                    <option value="Macaca mulatta">Macaca mulatta</option>
                    <option value="Macropus eugenii">Macropus eugenii</option>
                    <option value="Meleagris gallopavo">Meleagris gallopavo</option>
                    <option value="Microcebus murinus">Microcebus murinus</option>
                    <option value="Monodelphis domestica">Monodelphis domestica</option>
                    <option value="Mus musculus">Mus musculus</option>
                    <option value="Mustela putorius furo">Mustela putorius furo</option>
                    <option value="Myotis lucifugus">Myotis lucifugus</option>
                    <option value="Nomascus leucogenys">Nomascus leucogenys</option>
                    <option value="Ochotona princeps">Ochotona princeps</option>
                    <option value="Oreochromis niloticus">Oreochromis niloticus</option>
                    <option value="Ornithorhynchus anatinus">Ornithorhynchus anatinus</option>
                    <option value="Oryctolagus cuniculus">Oryctolagus cuniculus</option>
                    <option value="Oryzias latipes">Oryzias latipes</option>
                    <option value="Otolemur garnettii">Otolemur garnettii</option>
                    <option value="Pan troglodytes">Pan troglodytes</option>
                    <option value="Petromyzon marinus">Petromyzon marinus</option>
                    <option value="Pelodiscus sinensis">Pelodiscus sinensis</option>
                    <option value="Pongo abelii">Pongo abelii</option>
                    <option value="Procavia capensis">Procavia capensis</option>
                    <option value="Pteropus vampyrus">Pteropus vampyrus</option>
                    <option value="Rattus norvegicus">Rattus norvegicus</option>
                    <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option>
                    <option value="Sarcophilus harrisii">Sarcophilus harrisii</option>
                    <option value="Sorex araneus">Sorex araneus</option>
                    <option value="Sus scrofa">Sus scrofa</option>
                    <option value="Taeniopygia guttata">Taeniopygia guttata</option>
                    <option value="Takifugu rubripes">Takifugu rubripes</option>
                    <option value="Tarsius syrichta">Tarsius syrichta</option>
                    <option value="Tetraodon nigroviridis">Tetraodon nigroviridis</option>
                    <option value="Tupaia belangeri">Tupaia belangeri</option>
                    <option value="Tursiops truncatus">Tursiops truncatus</option>
                    <option value="Vicugna pacos">Vicugna pacos</option>
                    <option value="Xenopus tropicalis">Xenopus tropicalis</option>
                    <option value="Xiphophorus maculatus">Xiphophorus maculatus</option>
                </param>
            </when>
        </conditional>

        <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
            help="Allow peptides to contain up to this many missed enzyme cleavage sites. 2 is the recommended value"/>
        <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
            help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
            <options from_file="searchgui_mods.loc">
                <column name="name" index="0" />
                <column name="value" index="0" />
            </options>
        </param>
        <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" 
            help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
            <options from_file="searchgui_mods.loc">
                <column name="name" index="0" />
                <column name="value" index="0" />
            </options>
        </param>
        <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
        <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
        <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
            <option value="a">a</option>
            <option value="b" selected="true">b</option>
            <option value="c">c</option>
        </param>
        <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
            <option value="x">x</option>
            <option value="y" selected="true">y</option>
            <option value="z">z</option>
        </param>
        <conditional name="advanced">
            <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options">
                <option value="basic" selected="True">Basic</option>
                <option value="advanced">Advanced</option>
            </param>
            <when value="basic" />
            <when value="advanced">
                <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" />

                <conditional name="xtandem">
                    <param name="xtandem_selector" type="select" label="Run X!Tandem search">
                        <option value="yes" selected="True">Search with X!Tandem</option>
                        <option value="no">No X!Tandem search</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                    </when>
                </conditional>

                <conditional name="omssa">
                    <param name="omssa_selector" type="select" label="Run OMSSA search">
                        <option value="yes" selected="True">Search with OMSSA</option>
                        <option value="no">No OMSSA search</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
                        <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
                        <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" />
                    </when>
                </conditional>

                <conditional name="msgf">
                    <param name="msgf_selector" type="select" label="Run MSGF search">
                        <option value="yes" selected="True">Search with MSGF</option>
                        <option value="no">No MSGF search</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                    </when>
                </conditional>

                <conditional name="ms_amanda">
                    <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">
                        <option value="yes" selected="True">Search with MSGF</option>
                        <option value="no">No MS Amanda search</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                    </when>
                </conditional>
            </when>
        </conditional>
        <conditional name="processing_options">
            <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
                <option value="no" selected="True">Default Processing Options</option>
                <option value="yes">Advanced Processing Options</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
                <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
                <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
                <param name="protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="" type="float"
                    help="default 95%: '95.0' (-protein_fraction_mw_confidence)" />
                <conditional name="ptm_score">
                    <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
                        <option value="0" selected="True">A-score</option>
                        <option value="1">PhosphoRS</option>
                    </param>
                    <when value="0" />
                    <when value="1">
                        <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
                        <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="" type="float"
                            help="Automatic mode will be used if not set." />
                    </when>
                </conditional>
                <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
            </when>
        </conditional>
        <conditional name="filtering_options">
            <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
                help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s">
                <option value="no" selected="True">Default Filtering Options</option>
                <option value="yes">Advanced Processing Options</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
                <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />
                <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." />
                <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
                    <option value="0">ppm</option>
                    <option value="1">Daltons</option>
                </param>
                <param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" />
                <param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" />
                <param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="(-max_mascot_e)" />
                <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
            </when>
        </conditional>

        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
            <option value="3" selected="True">Peptide Report</option>
            <option value="4" selected="True">Protein Report</option>
            <option value="2">PSM Report</option>
            <option value="0">Certificate of Analysis</option>
            <option value="1">Hierarchical Report</option>
            <option value="cps">CPS file</option>
            <validator type="no_options" message="Please select at least one output file." />
        </param>
    </inputs>
    <outputs>
        <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
            <filter>'cps' in outputs</filter>
        </data>
        <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
            <filter>'0' in outputs</filter>
        </data>
        <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
            <filter>'2' in outputs</filter>
        </data>
        <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
            <filter>'3' in outputs</filter>
        </data>
        <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
            <filter>'4' in outputs</filter>
        </data>
        <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
            <filter>'1' in outputs</filter>
        </data>
    </outputs>
    <help>
**What it does**

Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results.

https://code.google.com/p/peptide-shaker/
https://code.google.com/p/searchgui/

**Reports**

*PSM Report*

Protein(s)	Protein(s) to which the peptide can be attached.
Sequence	Sequence of the peptide.
Variable Modifications	The variable modifications.
D-score	D-score for variable PTM localization.
probabilistic PTM score	The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
Localization Confidence	The confidence in variable PTM localization.
Fixed Modifications	The fixed modifications.
Spectrum File	The spectrum file.
Spectrum Title	The title of the spectrum.
Spectrum Scan Number	The spectrum scan number.
RT	Retention time
m/z	Measured m/z
Measured Charge	The charge as given in the spectrum file.
Identification Charge	The charge as inferred by the search engine.
Theoretical Mass	The theoretical mass of the peptide.
Isotope Number	The isotope number targetted by the instrument.
Precursor m/z Error	The precursor m/z matching error.
Score	Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
Confidence	Confidence in percent associated to the retained PSM.
Decoy	Indicates whether the peptide is a decoy (1: yes, 0: no).
Validation	Indicates the validation level of the protein group.


*Protein Report*

Main Accession	Main accession of the protein group.
Description	Description of the protein designed by the main accession.
Gene Name	The gene names of the Ensembl gene ID associated to the main accession.
Chromosome	The chromosome of the Ensembl gene ID associated to the main accession.
PI	Protein Inference status of the protein group.
Secondary Accessions	Other accessions in the protein group (alphabetical order).
Protein Group	The complete protein group (alphabetical order).
#Peptides	Total number of peptides.
#Validated Peptides	Number of validated peptides.
#Unique	Total number of peptides unique to this protein group.
#PSMs	Number of PSMs
#Validated PSMs	Number of validated PSMs
Coverage (%)	Sequence coverage in percent of the protein designed by the main accession.
Possible Coverage (%)	Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
MW (kDa)	Molecular Weight.
Spectrum Counting NSAF 	Normalized Spectrum Abundance Factor (NSAF)
Spectrum Counting emPAI	exponentially modified Protein Abundance Index (emPAI)
Confident Modification Sites, # Confident Modification Sites	List of the sites where a variable modification was confidently localized.
Other Modification Sites, # Other Modification Sites	List of the non-confident sites where a variable modification was localized.
Score	Score of the protein group.
Confidence	Confidence in percent associated to the protein group.
Decoy	Indicates whether the protein group is a decoy (1: yes, 0: no).
Validation	Indicates the validation level of the protein group.


*Peptide Report*


Protein(s)	Protein(s) to which this peptide can be attached.
AAs Before	The amino-acids before the sequence.
Sequence	Sequence of the peptide.
AAs After	The amino-acids after the sequence.
Modified Sequence	The peptide sequence annotated with variable modifications.
Variable Modifications	The variable modifications.
Localization Confidence	The confidence in PTMs localization.
Fixed Modifications	The fixed modifications.
#Validated PSMs	Number of validated PSMs.
#PSMs	Number of PSMs.
Score	Score of the peptide.
Confidence	Confidence in percent associated to the peptide.
Decoy	Indicates whether the peptide is a decoy (1: yes, 0: no).
Validation	Indicates the validation level of the protein group.


*Hirachical Report*

Main Accession	Main accession of the protein group.
Description	Description of the protein designed by the main accession.
PI	Protein Inference status of the protein group.
Secondary Accessions	Other accessions in the protein group (alphabetical order).
Protein Group	The complete protein group (alphabetical order).
#Peptides	Total number of peptides.
#Validated Peptides	Number of validated peptides.
#Unique	Total number of peptides unique to this protein group.
#PSMs	Number of PSMs
#Validated PSMs	Number of validated PSMs
Coverage (%)	Sequence coverage in percent of the protein designed by the main accession.
Possible Coverage (%)	Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
MW (kDa)	Molecular Weight.
Spectrum Counting NSAF 	Normalized Spectrum Abundance Factor (NSAF)
Spectrum Counting emPAI	exponentially modified Protein Abundance Index (emPAI)
Confident Modification Sites, # Confident Modification Sites	List of the sites where a variable modification was confidently localized.
Other Modification Sites, # Other Modification Sites	List of the non-confident sites where a variable modification was localized.
Score	Score of the protein group.
Confidence	Confidence in percent associated to the protein group.
Decoy	Indicates whether the protein group is a decoy (1: yes, 0: no).
Validation	Indicates the validation level of the protein group.
Protein(s)	Protein(s) to which this peptide can be attached.
AAs Before	The amino-acids before the sequence.
Sequence	Sequence of the peptide.
AAs After	The amino-acids after the sequence.
Variable Modifications	The variable modifications.
Localization Confidence	The confidence in PTMs localization.
Fixed Modifications	The fixed modifications.
#Validated PSMs	Number of validated PSMs.
#PSMs	Number of PSMs.
Score	Score of the peptide.
Confidence	Confidence in percent associated to the peptide.
Decoy	Indicates whether the peptide is a decoy (1: yes, 0: no).
Validation	Indicates the validation level of the protein group.
Protein(s)	Protein(s) to which the peptide can be attached.
Sequence	Sequence of the peptide.
Modified Sequence	The peptide sequence annotated with variable modifications.
Variable Modifications	The variable modifications.
D-score	D-score for variable PTM localization.
probabilistic PTM score	The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
Localization Confidence	The confidence in variable PTM localization.
Fixed Modifications	The fixed modifications.
Spectrum File	The spectrum file.
Spectrum Title	The title of the spectrum.
Spectrum Scan Number	The spectrum scan number.
RT	Retention time
m/z	Measured m/z
Measured Charge	The charge as given in the spectrum file.
Identification Charge	The charge as inferred by the search engine.
Theoretical Mass	The theoretical mass of the peptide.
Isotope Number	The isotope number targetted by the instrument.
Precursor m/z Error	The precursor m/z matching error.
Score	Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
Confidence	Confidence in percent associated to the retained PSM.
Decoy	Indicates whether the peptide is a decoy (1: yes, 0: no).
Validation	Indicates the validation level of the protein group.




------

**Citation**

For the underlying tool, please cite `TODO`

If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker
    </help>
</tool>