annotate peptide_shaker.xml @ 58:07ff622ec007 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23"

<tool id="peptide_shaker"
      name="Peptide Shaker"
      version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@"
      profile="20.01"
>

    <description>
        Perform protein identification using various search engines based on results from SearchGUI
    </description>
    <macros>
        <import>macros_basic.xml</import>
        <import>macros_modifications.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement>
        <requirement type="package">unzip</requirement>
    </requirements>
    <expand macro="stdio" />
    <!-- TODO: check trap comment.
    <command use_shared_home="false">
-->
    <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 $bin_dir = "bin"
        #set $exporting_followup_boolean = False
        ## TODO: Re-enable again when solving writing paths.txt to user-related folders and non-existing exportFactory.json file.
        ## trap ">&2 cat resources/*.log" EXIT;

        mkdir output_reports &&
        cwd=`pwd` &&
        export HOME=\$cwd &&

        ln -s '$searchgui_input' searchgui_input.zip &&

        ## OPTIONAL MAIN PARAMETERS
        ## If we have a specific Identification Parameters file to use, we will use it instead of the one provided in the search_gui file
        #if $optional_main_parameters.input_optional_identification_parameters:
            cp '${optional_main_parameters.input_optional_identification_parameters}' SEARCHGUI_IdentificationParameters.par &&
        #else:
            jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
        #end if
        ## Optional Fasta file
        #if $optional_main_parameters.input_fasta_file:
            ## copy the input .fasta file to the working folder
            cp '${optional_main_parameters.input_fasta_file}' './input_fasta_file.fasta' &&
        #end if
        ## Optional Spectrum files: if the user specified input spectra files, we use them
        ## NOTE: != None DOES NOT SEEM TO WORK ANYMORE ON MODERN GALAXIES
        #if str($optional_main_parameters.input_optional_spectrum_files) != 'None' and str($optional_main_parameters.input_optional_spectrum_files) != '':
            mkdir peaklist_input_files &&
            #for $peak_list_file in $optional_main_parameters.input_optional_spectrum_files:
                #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}' 'peaklist_input_files/${input_name}' &&
            #end for
        #end if

        #if str($exporting_options.output_reports) != "None" and str($exporting_options.output_reports) != ""
            #set $output_reports_list = set(str($exporting_options.output_reports).split(','))
        #else
            #set $output_reports_list = set()
	      #end if

        ######################
        ## PeptideShakerCLI ##
        ######################
        peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
            -gui 0
            -temp_folder \$cwd/PeptideShakerCLI
            -log \$cwd/resources
            -reference '$exp_str'
            -identification_files \$cwd/searchgui_input.zip
            -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
        #if $optional_main_parameters.input_fasta_file:
            -fasta_file './input_fasta_file.fasta'
        #end if
        #if str($optional_main_parameters.input_optional_spectrum_files) != 'None' and str($optional_main_parameters.input_optional_spectrum_files) != '':
            -spectrum_files  \$cwd/peaklist_input_files
        #end if

        #if $exporting_options.zip_conditional.zip_output_boolean == 'zip':
            -zip \$cwd/peptideshaker_output.zip
            -out \$cwd/peptideshaker_output.psdb
            #if $exporting_options.zip_conditional.export_mgf_when_zip:
                -output_mgf 1
    	    #end if
        #else:
            #if $exporting_options.zip_conditional.export_psdb:
                -out \$cwd/peptideshaker_output.psdb
            #end if
        #end if

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

        ##################################
        ## mzidCLI options ##
        ##################################

        #if $exporting_options.mzidentml_conditional.mzidentml_creation == 1:
            -output_file \$cwd/output.mzid
            -include_sequences ${exporting_options.mzidentml_conditional.include_sequences}
            #if $exporting_options.mzidentml_conditional.contact_options.contact_options_selector == "yes":
                -contact_first_name "$exporting_options.mzidentml_conditional.contact_options.contact_first_name"
                -contact_last_name "$exporting_options.mzidentml_conditional.contact_options.contact_last_name"
                -contact_email "$exporting_options.mzidentml_conditional.contact_options.contact_email"
                -contact_address "$exporting_options.mzidentml_conditional.contact_options.contact_address"
                #if str($exporting_options.mzidentml_conditional.contact_options.contact_url).strip() != '':
                    -contact_url = "$exporting_options.mzidentml_conditional.contact_options.contact_url"
                #end if
                -organization_name "$exporting_options.mzidentml_conditional.contact_options.organization_name"
                -organization_email "$exporting_options.mzidentml_conditional.contact_options.organization_email"
                -organization_address "$exporting_options.mzidentml_conditional.contact_options.organization_address"
                #if str($exporting_options.mzidentml_conditional.contact_options.organization_url).strip() != '':
                    -organization_url = "$exporting_options.mzidentml_conditional.contact_options.organization_url"
                #end if
            #else:
                -contact_first_name "Proteomics"
                -contact_last_name "Galaxy"
                -contact_email "[e-mail]"
                -contact_address "[e-mail]"
                -organization_name "University of Minnesota"
                -organization_email "[e-mail]"
                -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
            #end if
        #end if

        ####################################################################
        ##    PeptideShaker Identification Features Reports options       ##
        ####################################################################
        ## Generate Reports if the user has selected one of the 11 additional reports
        #if len($output_reports_list) > 0
                -out_reports \$cwd/output_reports
                -reports #echo ','.join($output_reports_list)#
        #end if

        ####################################################
        ##    PeptideShaker Follow-Up Analysis options    ##
        ####################################################
        ## TODO: When done in the app, export graph databases, TPP export, recalibrate espectra

        #if $exporting_options.followup_conditional.followup_conditional_selector == "yes"
            #if $exporting_options.followup_conditional.followup_export_spectra != "off"
                #set $exporting_followup_boolean = True
                -spectrum_folder \$cwd/output_reports -psm_type $exporting_options.followup_conditional.followup_export_spectra
            #end if
            #if $exporting_options.followup_conditional.followup_export_accession_numbers != "off"
                #set $exporting_followup_boolean = True
                -accessions_file \$cwd/output_reports/proteins_accession_numbers.txt -accessions_type $exporting_options.followup_conditional.followup_export_accession_numbers
            #end if
            #if $exporting_options.followup_conditional.followup_export_sequences != "off"
                #set $exporting_followup_boolean = True
                -sequences_file \$cwd/output_reports/proteins_sequences.fasta -sequences_type $exporting_options.followup_conditional.followup_export_sequences
            #end if
            #if $exporting_options.followup_conditional.followup_export_proteoforms != "off"
                #set $exporting_followup_boolean = True
                -proteoforms_file \$cwd/output_reports/proteins_proteoforms.txt
            #end if
            #if $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector != "off"
                #set $exporting_followup_boolean = True
                -progenesis_file \$cwd/output_reports/progenesis.txt -progenesis_type $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector
                #if $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector == "3"
                  #set $progenesis_ptms = $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_ptms or ''
                  #if $progenesis_ptms
                    -progenesis_ptms "$progenesis_ptms"
                  #end if
                #end if
            #end if
            #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector != "off"
                #set $exporting_followup_boolean = True
                -inclusion_list_file \$cwd/output_reports/inclusion_list.txt -inclusion_list_format $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector
                #set $peptide_filters = $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_peptide_filters or ''
                #if $peptide_filters
                  -inclusion_list_peptide_filters "$peptide_filters"
                #end if
                #set $protein_filters = $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_protein_filters or ''
                #if $protein_filters
                  -inclusion_list_protein_filters "$protein_filters"
                #end if
                #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window
                  -inclusion_list_rt_window $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window
                #end if
            #end if
        #end if

        ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
        #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean):
            ## This unzipping command creates a reports folder into the current folder!
            && unzip \$cwd/peptideshaker_output.zip "reports/*" -d \$cwd
            && mv reports/* output_reports
            && rm -r reports
        #end if

        ## If the user chose to export mgf file/s out of the zip file
        #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_mgf_when_zip:
          && mkdir output_mgf
          && mkdir output_cui
          && mv \$cwd/*.mgf output_mgf
          && mv \$cwd/*.cui output_cui
	      #end if

        ## Renaming identification features reports to findable names and moving them to the root folder
	      #if len(output_reports_list)>0:
            #if '0' in $output_reports_list:
                && find \$cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
            #end if
            #if '1' in $output_reports_list:
                && find \$cwd/output_reports -name '*Default_Hierarchical_Report.txt' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
            #end if
            #if '2' in $output_reports_list:
                && find \$cwd/output_reports -name '*Default_PSM_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
            #end if
            #if '3' in $output_reports_list:
                && find \$cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \;
            #end if
            #if '4' in $output_reports_list:
                && find \$cwd/output_reports -name '*Default_PSM_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "psm_nonvalidated.txt"' {} \;
            #end if
            #if '5' in $output_reports_list:
                && find \$cwd/output_reports -name '*Default_Peptide_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
            #end if
            #if '6' in $output_reports_list:
                && find \$cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
            #end if
            #if '7' in $output_reports_list:
                && find \$cwd/output_reports -name '*Default_Peptide_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "peptides_nonvalidated.txt"' {} \;
            #end if
            #if '8' in $output_reports_list:
                && find \$cwd/output_reports -name '*Default_Protein_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
            #end if
            #if '9' in $output_reports_list:
                && find \$cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
            #end if
            #if '10' in $output_reports_list:
                && find \$cwd/output_reports -name '*Default_Protein_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "proteins_nonvalidated.txt"' {} \;
            #end if
            #if '11' in $output_reports_list:
                && find \$cwd/output_reports -name '*Extended_PSM_Report.txt' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
            #end if
            ## the last ; is removed from the generated command line
            ## thus we need to make sure that the above `find ... -exec ... \;`
            ## is not the last command
            && true
        #end if

        ## Moving followup analysis to the root folder (it is necessary if zip option was not chosen, or it was chosen but also exporting out of the zip)
        #if $exporting_options.followup_conditional.followup_conditional_selector == "yes" and ($exporting_options.zip_conditional.zip_output_boolean != 'zip' or ($exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip)):
            ## Spectrum analysis are already expected to be into the output_reports folder itself
            #if $exporting_options.followup_conditional.followup_export_accession_numbers != "off"
                && mv \$cwd/output_reports/proteins_accession_numbers.txt \$cwd/proteins_accession_numbers.txt
            #end if
            #if $exporting_options.followup_conditional.followup_export_sequences != "off"
                && mv \$cwd/output_reports/proteins_sequences.fasta \$cwd/proteins_sequences.fasta
            #end if
            #if $exporting_options.followup_conditional.followup_export_proteoforms != "off"
                && mv \$cwd/output_reports/proteins_proteoforms.txt \$cwd/proteins_proteoforms.txt
            #end if
            #if $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector != "off"
                && mv \$cwd/output_reports/progenesis.txt \$cwd/progenesis.txt
            #end if
            #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector != "off"
                && mv \$cwd/output_reports/inclusion_list.txt \$cwd/inclusion_list.txt
            #end if
        #end if
]]>
    </command>
    <inputs>
        <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
            help="SearchGUI Results from History">
            <options options_filter_attribute="metadata.searchgui_major_version" >
                <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
            </options>
        </param>

        <section name="optional_main_parameters" expanded="false" title="Optional main parameters">
              <param format="json" name="input_optional_identification_parameters" type="data" label="Identification parameters" optional="true" help="This optional parameter file will be used instead of the default one"/>
              <param format="fasta" name="input_fasta_file" type="data" label="Fasta file" optional="true" help="This optional fasta file will be used instead of the one included in the SearchGUI file (if it exists). If the SearchGUI file does not include the fasta file, this parameter is must be considered as mandatory."/>
              <param format="mgf,mzml" name="input_optional_spectrum_files" type="data" label="Spectrum files" optional="true" multiple="true" help="Optional spectrum files will be used together with spectra included in the SearchGUI output"/>
        </section>

        <section name="exporting_options" expanded="true" title="Exporting options" help="All different outputs PeptideShaker may produce">

            <conditional name="zip_conditional">
                <param name="zip_output_boolean" type="boolean" truevalue="zip" falsevalue="separate" checked="false" label="Compress results into a single zip file" />
                <when value="separate">
                    <param name="export_psdb" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports PeptideShakers‘ .psdb file" />
                </when>
                <when value="zip">
                    <param name="export_reports_when_zip" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Also export reports out of the zip" />
                    <param name="export_mgf_when_zip" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Also export mgf file/s out of the zip" help=".cui index files are exported as a different collection too" />
                </when>
            </conditional>

            <conditional name="mzidentml_conditional">
                <param name="mzidentml_creation" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Creates a mzIdentML file" />
                <when value="1">
              	     <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in the mzIdentML file" />

                     <conditional name="contact_options">
                         <param name="contact_options_selector" type="select" label="Contact Information"
                             help="Create a Galaxy workflow to save these values">
                             <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
                             <option value="yes">Specify Contact Information</option>
                         </param>
                         <when value="no" />
                         <when value="yes">
                             <param name="contact_first_name" type="text" value="" label="Contact first name.">
                                 <validator type="regex" message="">\S+.*</validator>
                             </param>
                             <param name="contact_last_name" type="text" value="" label="Contact last name.">
                                 <validator type="regex" message="">\S+.*</validator>
                             </param>
                             <param name="contact_email" type="text" value="" label="Contact e-mail.">
                                 <validator type="regex" message="">\S+@\S+</validator>
                             </param>
                             <param name="contact_address" type="text" value="" label="Contact address.">
                                 <validator type="regex" message="">\S+.*</validator>
                             </param>
                             <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
                             </param>
                             <param name="organization_name" type="text" value="" label="Organization name.">
                                 <validator type="regex" message="">\S+.*</validator>
                             </param>
                             <param name="organization_email" type="text" value="" label="Organization e-mail.">
                                 <validator type="regex" message="">\S+@\S+</validator>
                             </param>
                             <param name="organization_address" type="text" value="" label="Organization address.">
                                 <validator type="regex" message="">\S+.*</validator>
                             </param>
                             <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
                             </param>
                         </when>
                     </conditional>

                </when>
                <when value="0" />
            </conditional>

            <!-- FOLLOW-UP REPORTS  -->
            <conditional name="followup_conditional">
                <param name="followup_conditional_selector" type="select" label="Follow-up analysis export options">
                    <option value="yes">Export follow-up analysis</option>
                    <option value="no" selected="True">Do not export</option>
                </param>
                <when value="no" />
                <when value="yes">
                    <param name="followup_export_spectra" label="Spectra: Export spectrum files as MGF" type="select" help="Commonly: spectra of Non-Validated PSMs">
                        <option value="0" >Spectra of Non-Validated PSMs</option>
                        <option value="1" >Spectra of Non-Validated Peptides</option>
                        <option value="2" >Spectra of Non-Validated Proteins</option>
                        <option value="3" >Spectra of Validated PSMs</option>
                        <option value="4" >Spectra of Validated PSMs of Validated Peptides</option>
                        <option value="5" >Spectra of validated PSMs of Validated Peptides of Validated Proteins</option>
                        <option value="off" selected="True">Do not export</option>
                    </param>
                    <param name="followup_export_accession_numbers" label="Proteins: Export accession numbers as TXT" type="select" help="Commonly: Main Accession of Validated Protein Groups">
                        <option value="0" >Main Accession of Validated Protein Groups</option>
                        <option value="1" >All Accessions of Validated Protein Groups</option>
                        <option value="2" >Non-Validated Accessions</option>
                        <option value="off" selected="True">Do not export</option>
                    </param>
                    <param name="followup_export_sequences" label="Proteins: Export protein details/sequences in fasta format" type="select" help="Commonly: Main Accession of Validated Protein Groups">
                        <option value="0" >Main Accession of Validated Protein Groups</option>
                        <option value="1" >All Accessions of Validated Protein Groups</option>
                        <option value="2" >Non-Validated Accessions</option>
                        <option value="off" selected="True">Do not export</option>
                    </param>
                    <param name="followup_export_proteoforms" label="Proteins: Export proteoforms as TXT" type="select">
                        <option value="on">Export</option>
                        <option value="off" selected="True">Do not export</option>
                    </param>
                    <conditional name="followup_export_progenesis_conditional">
                        <param name="followup_export_progenesis_selector" label="Label free quantification: Exports identification results in Progenesis LC-MS compatible format as TXT" type="select" help="Commonly: Validated PSMs of Validated Peptides of Validated Proteins">
                            <option value="0">Validated PSMs of Validated Peptides of Validated Proteins</option>
                            <option value="1">Validated PSMs of Validated Peptides</option>
                            <option value="2">Validated PSMs</option>
                            <option value="3">Confidently localized PTMs of Validated PSMs of Validated Peptides of Validated Proteins</option>
                            <option value="off" selected="True">Do not export</option>
                        </param>
                        <when value="0"/>
                        <when value="1"/>
                        <when value="2"/>
                        <when value="3">
                            <param name="followup_export_progenesis_ptms" type="select" label="Targeted PTMs" multiple="true"
                                help="">
                                <expand macro="modifications"/>
                            </param>
                        </when>
                        <when value="off"/>
                    </conditional>
                    <conditional name="followup_export_inclusion_list_conditional">
                        <param name="followup_export_inclusion_list_selector" label="Inclusion/Exclusion list: Exports a file for an inclusion list of validated hits" type="select" help="Commonly: Thermo">
                            <option value="0" >Thermo</option>
                            <option value="1" >ABI</option>
                            <option value="2" >Bruker</option>
                            <option value="3" >MassLynx</option>
                            <option value="off" selected="True">Do not export</option>
                        </param>
                        <when value="0">
                            <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
                                help="">
                                <option value="0">Miscleaved Peptides</option>
                                <option value="1">Reactive Peptides</option>
                                <option value="2">Degenerated Peptides</option>
                            </param>
                            <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
                                help="">
                                <option value="1">Related Proteins</option>
                                <option value="2">Related and Unrelated Proteins</option>
                                <option value="3">Unrelated Proteins</option>
                            </param>
                            <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
                                help=""/>
                        </when>
                        <when value="1">
                            <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
                                help="">
                                <option value="0">Miscleaved Peptides</option>
                                <option value="1">Reactive Peptides</option>
                                <option value="2">Degenerated Peptides</option>
                            </param>
                            <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
                                help="">
                                <option value="1">Related Proteins</option>
                                <option value="2">Related and Unrelated Proteins</option>
                                <option value="3">Unrelated Proteins</option>
                            </param>
                            <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
                                help=""/>
                        </when>
                        <when value="2">
                            <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
                                help="">
                                <option value="0">Miscleaved Peptides</option>
                                <option value="1">Reactive Peptides</option>
                                <option value="2">Degenerated Peptides</option>
                            </param>
                            <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
                                help="">
                                <option value="1">Related Proteins</option>
                                <option value="2">Related and Unrelated Proteins</option>
                                <option value="3">Unrelated Proteins</option>
                            </param>
                            <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
                                help=""/>
                        </when>
                        <when value="3">
                            <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
                                help="">
                                <option value="0">Miscleaved Peptides</option>
                                <option value="1">Reactive Peptides</option>
                                <option value="2">Degenerated Peptides</option>
                            </param>
                            <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
                                help="">
                                <option value="1">Related Proteins</option>
                                <option value="2">Related and Unrelated Proteins</option>
                                <option value="3">Unrelated Proteins</option>
                            </param>
                            <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
                                help=""/>
                        </when>
                        <when value="off"/>
                    </conditional>
                </when>
            </conditional>

            <!-- IDENTIFICATION FEATURES REPORTS  -->
            <param name="output_reports" type="select" display="checkboxes" multiple="True" optional="true" label="Identification features reports to be generated">
                <option value="3">PSM Report</option>
                <option value="4">PSM Report with non-validated matches</option>
                <option value="2">PSM Phosphorylation Report</option>
                <option value="11">Extended PSM Report</option>
                <option value="6">Peptide Report</option>
                <option value="7">Peptide Report with non-validated matches</option>
                <option value="5">Peptide Phosphorylation Report</option>
                <option value="9">Protein Report</option>
                <option value="10">Protein Report with non-validated matches</option>
                <option value="8">Protein Phosphorylation Report</option>
                <option value="0">Certificate of Analysis</option>
                <option value="1">Hierarchical Report</option>
            </param>

        </section>

    </inputs>
    <outputs>
        <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
            <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True</filter>
        </data>
        <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
            <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['mzidentml_conditional']['mzidentml_creation'] is True</filter>
        </data>
        <data format="peptideshaker_archive" name="output_psdb" from_work_dir="peptideshaker_output.psdb" label="${tool.name} on ${on_string}: PSDB file">
            <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_psdb'] is True</filter>
        </data>
        <collection name="output_mgf" type="list" label="${tool.name} on ${on_string}: Mgf" >
            <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_mgf_when_zip'] is True</filter>
            <discover_datasets pattern="__name_and_ext__" directory="output_mgf" ext="mgf"/>
        </collection>
        <collection name="output_cui" type="list" label="${tool.name} on ${on_string}: Cui" >
            <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_mgf_when_zip'] is True</filter>
            <discover_datasets pattern="__name_and_ext__" directory="output_cui" ext="cui"/>
        </collection>

        <!-- Follow-up analysis -->
        <collection name="output_spectra" type="list" label="${tool.name} on ${on_string}: Spectra" >
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_spectra'] != 'off' </filter>
            <discover_datasets pattern="__name_and_ext__" directory="output_reports" ext="mgf"/>
        </collection>
        <data format="txt" name="output_proteins_accessions" from_work_dir="proteins_accession_numbers.txt" label="${tool.name} on ${on_string}: Proteins Accession Numbers">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_accession_numbers'] != 'off' </filter>
        </data>
        <data format="fasta" name="output_proteins_sequences" from_work_dir="proteins_sequences.fasta" label="${tool.name} on ${on_string}: Proteins Sequences">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_sequences'] != 'off' </filter>
        </data>
        <data format="txt" name="output_proteoforms" from_work_dir="proteins_proteoforms.txt" label="${tool.name} on ${on_string}: Proteins Proteoforms">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_proteoforms'] != 'off' </filter>
        </data>
        <data format="txt" name="output_progenesis" from_work_dir="progenesis.txt" label="${tool.name} on ${on_string}: Progenesis">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_progenesis_conditional']['followup_export_progenesis_selector'] != 'off' </filter>
        </data>
        <data format="txt" name="output_inclusion_list" from_work_dir="inclusion_list.txt" label="${tool.name} on ${on_string}: Inclusion/Exclusion List">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_inclusion_list_conditional']['followup_export_inclusion_list_selector'] != 'off' </filter>
        </data>

        <!-- Identification Features outputs -->
	      <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Certificate of Analysis">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '0' in exporting_options['output_reports']</filter>
        </data>
        <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '1' in exporting_options['output_reports']</filter>
        </data>
        <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '2' in exporting_options['output_reports']</filter>
        </data>
        <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '3' in exporting_options['output_reports']</filter>
        </data>
        <data format="tabular" name="output_psm_nonvalidated" from_work_dir="psm_nonvalidated.txt" label="${tool.name} on ${on_string}: PSM Report with non-validated matches">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '4' in exporting_options['output_reports']</filter>
        </data>
        <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '11' in exporting_options['output_reports']</filter>
        </data>
        <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '5' in exporting_options['output_reports']</filter>
        </data>
        <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '6' in exporting_options['output_reports']</filter>
        </data>
        <data format="tabular" name="output_peptides_nonvalidated" from_work_dir="peptides_nonvalidated.txt" label="${tool.name} on ${on_string}: Peptide Report with non-validated matches">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '7' in exporting_options['output_reports']</filter>
        </data>
        <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '8' in exporting_options['output_reports']</filter>
        </data>
        <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '9' in exporting_options['output_reports']</filter>
        </data>
        <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Report with non-validated matches">
            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '10' in exporting_options['output_reports']</filter>
        </data>
    </outputs>

    <tests>
      <!-- Basic test: default identification parameters, searchgui_tinydb1.fasta, 4 search engines xx-->
      <test expect_num_outputs="2">
          <param name="searchgui_input" value="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive"/>
          <param name="mzidentml_creation" value="1"/>
          <param name="export_psdb" value="1"/>
          <output name="mzidentML" ftype="mzid">
              <assert_contents>
                  <has_text text="MzIdentML"/>
              </assert_contents>
          </output>
          <output name="output_psdb" ftype="peptideshaker_archive">
              <assert_contents>
                  <has_size value="122880" delta="3000"/>
              </assert_contents>
          </output>
      </test>

      <!-- Modifications test: default identification parameters with modifications, searchgui_tinydb1.fasta, 4 search engines -->
      <test expect_num_outputs="1">
          <param name="searchgui_input" value="searchgui_tiny_result_default_4engines_modifications.zip" ftype="searchgui_archive"/>
          <param name="mzidentml_creation" value="0"/>
          <param name="export_psdb" value="1"/>
          <output name="output_zip" ftype="peptideshaker_archive">
              <assert_contents>
                  <has_size value="126976" delta="3000"/>
              </assert_contents>
          </output>
      </test>

      <!-- Reports tests: default identification parameters, small spectra, some search engines (XTandem,MSGF+, OMSSA), all identification reports -->
      <test expect_num_outputs="12">
          <param name="searchgui_input" value="searchgui_smallsearch_default_somesearchengines_modifications.zip" ftype="searchgui_archive"/>
          <param name="mzidentml_creation" value="0"/>
          <param name="zip_output_boolean" value="separate"/>
          <param name="export_psdb" value="0"/>
          <param name="output_reports" value="0,1,2,3,4,5,6,7,8,9,10,11"/>
          <output name="output_certificate" file="peptideshaker_reports_output_certificate.txt" ftype="txt" lines_diff="8"/>
          <output name="output_hierarchical" file="peptideshaker_reports_output_hierarchical.tabular" ftype="tabular"/>
          <output name="output_extended_psm" file="peptideshaker_reports_output_extendedpsm.tabular" ftype="tabular"/>
          <output name="output_psm" file="peptideshaker_reports_output_psm.tabular" ftype="tabular"/>
          <output name="output_psm_phosphorylation" file="peptideshaker_reports_output_psmphosphorylation.tabular" ftype="tabular"/>
          <output name="output_psm_nonvalidated" file="peptideshaker_reports_output_psmnonvalidated.tabular" ftype="tabular"/>
          <output name="output_peptides" file="peptideshaker_reports_output_peptides.tabular" ftype="tabular"/>
          <output name="output_peptides_phosphorylation" file="peptideshaker_reports_output_peptidesphosphorylation.tabular" ftype="tabular"/>
          <output name="output_peptides_nonvalidated" file="peptideshaker_reports_output_peptidesnonvalidated.tabular" ftype="tabular"/>
          <output name="output_proteins" file="peptideshaker_reports_output_proteins.tabular" ftype="tabular"/>
          <output name="output_proteins_phosphorylation" file="peptideshaker_reports_output_proteinsphosphorylation.tabular" ftype="tabular"/>
          <output name="output_proteins_nonvalidated" file="peptideshaker_reports_output_proteinsnonvalidated.tabular" ftype="tabular"/>
      </test>

      <!-- followup analysis tests: default identification parameters, small spectra, some search engines (XTandem,MSGF+, OMSSA), all followup analysis -->
      <test expect_num_outputs="5">
          <param name="searchgui_input" value="searchgui_smallsearch_default_somesearchengines_modifications.zip" ftype="searchgui_archive"/>
          <param name="mzidentml_creation" value="0"/>
          <param name="zip_output_boolean" value="separate"/>
          <param name="export_psdb" value="0"/>
          <param name="followup_conditional_selector" value="yes"/>
          <param name="followup_export_spectra" value="0"/>
          <param name="followup_export_accession_numbers" value="0"/>
          <param name="followup_export_sequences" value="0"/>
          <param name="followup_export_proteoforms" value="on"/>
          <param name="followup_export_progenesis_selector" value="0"/>
          <output_collection name="output_spectra" type="list">
              <element name="searchgui_smallspectra_non_validated_PSMs" ftype="mgf">
                  <assert_contents>
                      <has_line_matching expression="236.0470428 11.674492836"/>
                      <has_line_matching expression="520.9862671 4666.4399414063"/>
                      <has_line_matching expression="267.4349976 50.7710571289"/>
                      <has_line_matching expression="665.7418213 3.8165459633"/>
                      <has_line_matching expression="634.7792969 2367.6374511719"/>
                  </assert_contents>
              </element>
          </output_collection>
          <output name="output_proteins_accessions" ftype="txt">
              <assert_contents>
                  <has_line_matching expression="cds.comp41779_c0_seq1"/>
                  <has_line_matching expression="cds.comp41890_c0_seq1"/>
                  <has_line_matching expression="cds.comp41890_c0_seq1_REVERSED"/>
                  <has_line_matching expression="cds.comp8310_c0_seq2"/>
              </assert_contents>
          </output>
          <output name="output_proteins_sequences" ftype="fasta">
              <assert_contents>
                  <has_line_matching expression=">generic|cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-6"/>
                  <has_line_matching expression="METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT"/>
                  <has_line_matching expression="generic|cds.comp41890_c0_seq1_REVERSED|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED"/>
                  <has_line_matching expression="LNYTTELNYTAKEDGRTNLLVTNVKAGVGLRSKNHWVLDGSNPDGMGNAWVKAFGGPKLVLNEIEYESIDINDSNQMIKWGSLDVTHSNSTNELLIFSGDRDTESIAVPGKNNKRYTSHEQLEGKVLAPTPSQY"/>
              </assert_contents>
          </output>
          <output name="output_proteoforms" ftype="txt">
              <assert_contents>
                  <has_line_matching expression="cds.comp8310_c0_seq2"/>
                  <has_line_matching expression="cds.comp41890_c0_seq1_REVERSED"/>
                  <has_line_matching expression="cds.comp41779_c0_seq1"/>
                  <has_line_matching expression="cds.comp41779_c0_seq2"/>
                  <has_line_matching expression="cds.comp41779_c0_seq3"/>
              </assert_contents>
          </output>
          <output name="output_progenesis" ftype="txt">
              <assert_contents>
                  <has_text_matching expression="NLVAEESMNMLKNK\t:::::::::::::::\t100.0\tcds.comp8310_c0_seq2\tm.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16\tsmall.17.17."/>
                  <has_text_matching expression="LDRLISATSISPEHKIDFLFK\t::::::::::::::::::::::\t100.0\tcds.comp41779_c0_seq1\tm.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67\tsmall.3.3."/>
                  <has_n_columns n="8" />
              </assert_contents>
          </output>

      </test>

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

PeptideShaker is a search engine for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML.

http://compomics.github.io/projects/peptide-shaker.html

----

Outputs
=======

*zip*
------

When choosing zip option, all other outputs are compressed and included into the zip file and, by default, no other file is shown in the Galaxy history. This last behaviour may be changed in order to have all other outputs also available in the history.

*psdb*
------

psdb is the native format used by PeptideShaker. It contains all the information required by PeptideShaker to run.

*mzIdentML*
-----------

PeptideShaker can load results from virtually any identification algorithm in the mzIdentML format as long as the minimal peptide to spectrum match information is present in the file.

The following is required:

• Spectrum file format has to be mgf.
• Each PSM has a score or e-value as a PSM score CV term.


*Follow-up analysis*
--------------------

Spectra
'''''''

Exports the spectra according to the category of the PSMs:

• Spectra of Non-Validated PSMs
• Spectra of Non-Validated Peptides
• Spectra of Non-Validated Proteins
• Spectra of Validated PSMs
• Spectra of Validated PSMs of Validated Peptides
• Spectra of validated PSMs of Validated Peptides of Validated Proteins.

Exported results are in mgf format.

Proteins: Accession numbers
'''''''''''''''''''''''''''

Export the protein accessions according to the category of the proteins:

• Main Accession of Validated Protein Groups
• All Accessions of Validated Protein Groups
• Non-Validated Accessions

Exported protein accessions are text format as TXT.


Proteins: Sequences
'''''''''''''''''''

Exports the protein details according to a category of proteins:

• Main Accession of Validated Protein Groups
• All Accessions of Validated Protein Groups
• Non-Validated Accessions.

Exported protein details are in fasta format.


Proteins: Proteoforms
'''''''''''''''''''''

Exports all possible proteoforms of the validated proteins.

Exported results are in text format as TXT.
Results file can be easily imported and used by PathwayMatcher_ tool.

.. _PathwayMatcher: https://toolshed.g2.bx.psu.edu/repository?repository_id=6d75f02b86acc421


Label free quantification
'''''''''''''''''''''''''

Exports the spectra from different categories of PSMs according to the export type:

• Validated PSMs of Validated Peptides of Validated Proteins
• Validated PSMs of Validated Peptides
• Validated PSMs
• Confidently localized PTMs of Validated PSMs of Validated Peptides of Validated Proteins

Exported identification results are in Progenesis LC-MS compatible format as TXT.


Inclusion/Exclusion list
''''''''''''''''''''''''

Exports an inclusion list of validated hits.

Inclusion list may be filtered according to peptide types:

• Miscleaved Peptides
• Reactive Peptides
• Degenerated Peptides.

and also according to protein inferences:

• Related Proteins
• Related and Unrelated Proteins
• Unrelated Proteins.

Finally, a retention time window may be established as a final filter.

Exported results can be in Thermo, ABI, Bruker or MassLynx formats.



*Identification Features Reports*
---------------------------------

PSM Report
''''''''''
=============================  ========================================
  Column                        Description
=============================  ========================================
 Protein(s)                     Protein(s) to which the peptide can be attached
 Sequence                       Sequence of the peptide
 AAs Before                     The amino acids before the sequence
 AAs After                      The amino acids after the sequence
 Position                       Position of the peptide in the protein sequence(s).
 Modified Sequence              The amino acids sequence annotated with variable modifications.
 Variable Modifications         The variable modifications
 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 [ppm]      The precursor m/z matching error.
 Localization Confidence        The confidence in variable PTM localization.
 probabilistic PTM score        The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
 D-score                        D-score for variable PTM localization
 Confidence                     Confidence in percent associated to the retained PSM.
 Validation                     Indicates the validation level of the protein group.
=============================  ========================================


PSM Report with non-validated matches
'''''''''''''''''''''''''''''''''''''

Same columns as the original PSM report but also includes non-validated matches.


PSM Phosphorylation Report
''''''''''''''''''''''''''
=============================  =========================================================
  Column                        Description
=============================  =========================================================
Protein(s)                     Protein(s) to which the peptide can be attached
Sequence                       Sequence of the peptide
Variable Modifications         The variable modifications
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 [ppm]      The precursor m/z matching error.
Localization Confidence        The confidence in variable PTM localization.
probabilistic PTM score        The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
D-score                        D-score for variable PTM localization
Confident Phosphosites	       List of the sites where a phosphorylation was confidently localized.
#Confident Phosphosites        Number of confidently localized phosphorylations.
Ambiguous Phosphosites	       List of the sites where a phosphorylation was ambiguously localized.
#Ambiguous Phosphosites	       Number of ambiguously localized phosphorylations.
Confidence [%]                 Confidence in percent associated to the retained PSM.
Validation                     Indicates the validation level of the protein group.
=============================  =========================================================


Extended PSM Report
'''''''''''''''''''

Same as the ordinary PSM report but adds a ``Decoy`` column and lacks the ``Confidence`` column.

=============================  =========================================================
  Extra column                  Description
=============================  =========================================================
  Decoy	                        Indicates whether the peptide is a decoy (1: yes, 0: no).

=============================  =========================================================



Peptide Report
''''''''''''''

==========================================  =====================================================
  Column                                     Description
==========================================  =====================================================
Protein(s):		                               Protein(s) to which this peptide can be attached.
Protein Group(s)                             List of identified protein groups this peptide can map to with associated validation level.
#Validated Protein Group(s)	                 Indicates the number of protein groups this peptide maps to.
Unique Group	                               Indicates whether the peptide maps to a unique protein group.
Sequence	                                   Sequence of the peptide.
Modified Sequence	                           The peptide sequence annotated with variable modifications.
Position	                                   Position of the peptide in the protein sequence(s).
AAs Before	                                 The amino acids before the sequence.
AAs After                                    The amino acids after the sequence.
Variable Modifications	                     The variable modifications.
Fixed Modifications	                         The fixed modifications.
Localization Confidence                      The confidence in PTMs localization.
#Validated PSMs	                             Number of validated PSMs.
#PSMs	                                       Number of PSMs.
Confidence [%]	                             Confidence in percent associated to the peptide.
Validation	                                 Indicates the validation level of the peptide.
==========================================  =====================================================


Peptide Report with non-validated matches
'''''''''''''''''''''''''''''''''''''''''

Same columns as the original Peptide report but also includes non-validated matches.


Peptide Phosphorylation Report
''''''''''''''''''''''''''''''

==========================================  =====================================================
  Column                                     Description
==========================================  =====================================================
Protein(s):		                               Protein(s) to which this peptide can be attached.
Protein Group(s)                             List of identified protein groups this peptide can map to with associated validation level.
#Validated Protein Group(s)	                 Indicates the number of protein groups this peptide maps to.
Unique Group	                               Indicates whether the peptide maps to a unique protein group.
Sequence	                                   Sequence of the peptide.
Modified Sequence	                           The peptide sequence annotated with variable modifications.
AAs Before	                                 The amino acids before the sequence.
AAs After                                    The amino acids after the sequence.
Variable Modifications	                     The variable modifications.
Fixed Modifications	                         The fixed modifications.
Localization Confidence                      The confidence in PTMs localization.
Confident Phosphosites	                     List of the sites where a phosphorylation was confidently localized.
#Confident Phosphosites	                     Number of confidently localized phosphorylations.
Ambiguous Phosphosites	                     List of the sites where a phosphorylation was ambiguously localized.
#Ambiguous Phosphosites	                     Number of ambiguously localized phosphorylations.
#Validated PSMs	                             Number of validated PSMs.
#PSMs	                                       Number of PSMs.
Confidence [%]	                             Confidence in percent associated to the peptide.
Validation	                                 Indicates the validation level of the peptide.
==========================================  =====================================================


Protein Report
''''''''''''''

==========================================  =====================================================
  Column                                     Description
==========================================  =====================================================
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.
MW (kDa)                                     Molecular Weight.
Possible Coverage (%)                        Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
Coverage (%)	                               Sequence coverage in percent of the protein designed by the main accession.
Spectrum Counting                            The selected spectrum counting metric.
Confidently Localized Modification Sites	   List of the sites where a variable modification was confidently localized.
# Confidently Localized Modification Sites	 Number of sites where a variable modification was confidently localized.
Ambiguously Localized Modification Sites	   List of the sites where ambiguously localized variable modification could possibly be located.
#Ambiguously Localized Modification Sites	   Number of ambiguously localized modifications.
Protein Inference	                           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).
#Validated Peptides                          Number of validated peptides.
#Peptides                                    Total number of peptides.
#Unique                                      Total number of peptides unique to this protein group.
#Validated Unique	                           Total number of peptides unique to this protein group.
#Validated PSMs                              Number of validated PSMs.
#PSMs                                        Number of PSMs.
Confidence [%]	                             Confidence in percent associated to the protein group.
Validation                                   Indicates the validation level of the protein group.
==========================================  =====================================================


Protein Report with non-validated matches
'''''''''''''''''''''''''''''''''''''''''

Same columns as the original Protein report but also includes non-validated matches.


Protein Phosphorylation Report
''''''''''''''''''''''''''''''

==========================================  =====================================================
  Column                                     Description
==========================================  =====================================================
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.
MW (kDa)                                     Molecular Weight.
Possible Coverage (%)                        Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
Coverage (%)	                               Sequence coverage in percent of the protein designed by the main accession.
Spectrum Counting NSAF	                     Raw Normalized Spectrum Abundance Factor (NSAF).
Confident Phosphosites	                     List of the sites where a phosphorylation was confidently localized.
#Confident Phosphosites	                     Number of sites where a phosphorylation was confidently localized.
Ambiguous Phosphosites	                     List of the sites where a phosphorylation was ambiguously localized.
#Ambiguous Phosphosites	                     Number of sites where a phosphorylation was ambiguously localized.
Protein Inference	                           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).
#Validated Peptides                          Number of validated peptides.
#Peptides                                    Total number of peptides.
#Unique                                      Total number of peptides unique to this protein group.
#Validated Unique	                           Total number of peptides unique to this protein group.
#Validated PSMs                              Number of validated PSMs.
#PSMs                                        Number of PSMs.
Confidence [%]	                             Confidence in percent associated to the protein group.
Validation                                   Indicates the validation level of the protein group.
==========================================  =====================================================


Certificate of Analysis
'''''''''''''''''''''''

Presents a summary of the most important statistics of the search, grouped by:

* Project Details:
    ‣ PeptideShaker Version, Date, Experiment, Sample, Replicate Number, Identification Algorithms.
* Database Search Parameters:
    ‣ Precursor Tolerance Unit, Precursor Ion m/z Tolerance, Fragment Ion Tolerance Unit, Fragment Ion m/z Tolerance, Cleavage, Enzyme, Missed Cleavages, Specificity, Database, Forward Ion, Rewind Ion, Fixed Modifications, Variable Modifications, Refinement Variable Modifications, Refinement Fixed Modifications.
* Input Filters:
    ‣ Minimal Peptide Length, Maximal Peptide Length, Precursor m/z Tolerance, Precursor m/z Tolerance Unit, Unrecognized Modifications Discarded.
* Validation Summary:
    • Proteins:
        ‣ #Validated, Total Possible TP, FDR Limit [%], FNR Limit [%], Confidence Limit, PEP Limit [%], Confidence Accuracy [%].
    • Peptides:
        ‣ #Validated, Total Possible TP, FDR Limit [%], FNR Limit [%], Confidence Limit [%], PEP Limit [%], Confidence Accuracy [%].
    • PSMs:
        ‣ #Validated PSM, Total Possible TP, FDR Limit [%]: PSMs, Confidence Limit [%], PEP Limit [%], Confidence Accuracy [%].
* PTM Scoring Settings:
    ‣ Probabilistic Score, Accounting for Neutral Losses, Threshold.
* Spectrum Counting Parameters:
    ‣ Method, Validated Matches Only
* Annotation Settings:
    ‣ Intensity Limit, Automatic Annotation, Selected Ions, Neutral Losses, Neutral Losses Sequence Dependence, Fragment Ion m/z Tolerance.


Hierachical Report
''''''''''''''''''

==========================================  =====================================================
  Column                                     Description
==========================================  =====================================================
Main Accession                               Main accession of the protein group.
Description	                                 Description of the protein designed by the main accession.
MW (kDa)                                     Molecular Weight.
Possible Coverage (%)                        Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
Coverage (%)                                 Sequence coverage in percent of the protein designed by the main accession.
Spectrum Counting NSAF                       Normalized Spectrum Abundance Factor (NSAF)
Confidently Localized Modification Sites	   List of the sites where a variable modification was confidently localized.
# Confidently Localized Modification Sites	 Number of sites where a variable modification was confidently localized.
Ambiguously Localized Modification Sites	   List of the sites where ambiguously localized variable modification could possibly be located.
#Ambiguously Localized Modification Sites	   Number of ambiguously localized modifications.
Protein Inference	                           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).
#Validated Peptides                          Number of validated peptides.
#Peptides                                    Total number of peptides.
#Unique                                      Total number of peptides unique to this protein group.
#Validated PSMs                              Number of validated PSMs
#PSMs                                        Number of PSMs
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.
==========================================  =====================================================

------

**Citation**

To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://compomics.github.io

If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
    </help>
    <expand macro="citations" />
</tool>