<tool id="peptide_shaker" name="Peptide Shaker" version="1.13.6">
    <description>
        Perform protein identification using various search engines based on results from SearchGUI
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.13.6">peptide-shaker</requirement>
    </requirements>
    <expand macro="stdio" />
    <command>
<![CDATA[
        #from datetime import datetime
        #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
        #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
        #set $temp_stderr = "peptideshaker_stderr"
        #set $bin_dir = "bin"


        mkdir output_reports;
        cwd=`pwd`;

        ln -s '$searchgui_input' searchgui_input.zip &&
        jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
        ######################
        ## PeptideShakerCLI ##
        ######################
        (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI
            --exec_dir="\$cwd/${bin_dir}"
            -temp_folder \$cwd/PeptideShakerCLI
            -experiment '$exp_str'
            -sample '$samp_str'
            -replicate 1
            -identification_files \$cwd/searchgui_input.zip
            -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
            -out \$cwd/peptideshaker_output.cpsx
            -zip \$cwd/peptideshaker_output.zip

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

            ##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 "${processing_options.protein_fraction_mw_confidence}"
                -ptm_alignment "${processing_options.ptm_alignment}"
            #end if

           ##Optional filtering parameters:
            #if $filtering_options.filtering_options_selector == "yes":
                -import_peptide_length_min "${filtering_options.min_peptide_length}"
                -import_peptide_length_max "${filtering_options.max_peptide_length}"
                -import_precurosor_mz "${filtering_options.max_precursor_error}"
                -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
                ##-max_xtandem_e "${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

        2>> $temp_stderr)

        &&

        echo "Running Reports";

        ##################################
        ## PeptideShaker Report options ##
        ##################################

        #if 'mzidentML' in str($outputs).split(','):
            echo "Generating mzIdentML";
            (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
                --exec_dir="\$cwd/${bin_dir}"
                -in \$cwd/peptideshaker_output.zip
                -output_file output.mzid
                #if $contact_options.contact_options_selector == "yes":
                    -contact_first_name "$contact_options.contact_first_name"
                    -contact_last_name "$contact_options.contact_last_name"
                    -contact_email "$contact_options.contact_email"
                    -contact_address "$contact_options.contact_address"
                    #if str($contact_options.contact_url).strip() != '':
                        -contact_url = "$contact_options.contact_url"
                    #end if
                    -organization_name "$contact_options.organization_name"
                    -organization_email "$contact_options.organization_email"
                    -organization_address "$contact_options.organization_address"
                    #if str($contact_options.organization_url).strip() != '':
                        -organization_url = "$contact_options.organization_url"
                    #end if
                #else:
                    -contact_first_name "Proteomics"
                    -contact_last_name "Galaxy"
                    -contact_email "galaxyp@umn.edu"
                    -contact_address "galaxyp@umn.edu"
                    -organization_name "University of Minnesota"
                    -organization_email "galaxyp@umn.edu"
                    -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
                #end if
            2>> $temp_stderr) 
            &&
        #end if

        ## Generate Reports if the user has selected one of the 8 additional reports
        ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker 
        ## and will not be passed to the command line
        #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):

            (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI
                --exec_dir="\$cwd/${bin_dir}"
                -temp_folder \$cwd/ReportCLI
                -in \$cwd/peptideshaker_output.zip
                -out_reports \$cwd/output_reports
                #set $cleaned_list = str($outputs).split(',')
                #if 'cps' in $cleaned_list:
                    #silent $cleaned_list.remove('cps')
                #end if
                #if 'mzidentML' in $cleaned_list:
                    #silent $cleaned_list.remove('mzidentML')
                #end if
                #if 'zip' in $cleaned_list:
                    #silent $cleaned_list.remove('zip')
                #end if
                ## Only numbers are left over. These corresponds to different reports.
                -reports #echo ','.join($cleaned_list)#

            2>> $temp_stderr)
            &&
        #end if

        ## # ls -l \$cwd/output_reports/* ;

        #if '0' in str($outputs).split(','):
            find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
            ;
        #end if
        #if '1' in str($outputs).split(','):
            find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
            ;
        #end if
        #if '2' in str($outputs).split(','):
            find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
            ;
        #end if
        #if '8' in str($outputs).split(','):
            find \$cwd/output_reports -name '*Extended_PSM_Report*' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
            ;
        #end if
        #if '3' in str($outputs).split(','):
            find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
            ;
        #end if
        #if '4' in str($outputs).split(','):
            find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
            ;
        #end if
        #if '5' in str($outputs).split(','):
            find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
            ;
        #end if
        #if '6' in str($outputs).split(','):
            find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
            ;
        #end if
        #if '7' in str($outputs).split(','):
            find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
            ;
        #end if

        exit_code_for_galaxy=\$?;
        cat $temp_stderr 2>&1;
        (exit \$exit_code_for_galaxy)

]]>
    </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>
        <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" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot"
                    help="default 95%: '95.0'" />
                <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" optional="true" value="" type="float"
                            help="Automatic mode will be used if not set" />
                    </when>
                </conditional>
                <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
                <!-- 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 Filtering Options</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" />
                <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" />
                <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10"
                    help="Next option specifies units (Da or ppm)" />
                <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
                    <option value="1">ppm</option>
                    <option value="0">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="" /-->
                <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
            </when>
        </conditional>
        <conditional name="contact_options">
            <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML"
                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>

        <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in mzIdentML" />
        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
            <option value="zip">Zip File for import to Desktop App</option>
            <option value="mzidentML" selected="True">mzidentML File</option>
            <option value="3">PSM Report</option>
            <option value="8">Extended PSM Report</option>
            <option value="2">PSM Phosphorylation Report</option>
            <option value="5">Peptide Report</option>
            <option value="4">Peptide Phosphorylation Report</option>
            <option value="7">Protein Report</option>
            <option value="6">Protein Phosphorylation 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="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
            <filter>'mzidentML' in outputs</filter>
        </data>
        <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
            <filter>'cps' in outputs</filter>
        </data>
        <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
            <filter>'zip' in outputs</filter>
        </data>
        <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
            <filter>'0' in outputs</filter>
        </data>
        <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
            <filter>'1' in outputs</filter>
        </data>
        <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
            <filter>'2' in outputs</filter>
        </data>
        <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
            <filter>'3' in outputs</filter>
        </data>
        <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
            <filter>'8' in outputs</filter>
        </data>
        <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
            <filter>'4' in outputs</filter>
        </data>
        <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
            <filter>'5' in outputs</filter>
        </data>
        <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
            <filter>'6' in outputs</filter>
        </data>
        <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
            <filter>'7' in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
            <param name="processing_options_selector" value="no"/>
            <param name="filtering_options_selector" value="no"/>
            <param name="outputs" value="zip,3"/>
            <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="900" />
            <output name="output_psm">
                <assert_contents>
                    <has_text text="cds.comp41779_c0_seq1" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
            <param name="processing_options_selector" value="no"/>
            <param name="filtering_options_selector" value="yes"/>
            <param name="min_peptide_length" value="1"/>
            <param name="outputs" value="0,1,2,3,4,5,6,7"/>
            <output name="output_certificate">
                <assert_contents>
                    <has_text text="Tolerance: 100" />
                    <has_text text="Carbamidomethylation of C" />
                </assert_contents>
            </output>
            <output name="output_hierarchical">
                <assert_contents>
                    <has_text_matching expression="1.1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2" />
                </assert_contents>
            </output>
            <output name="output_psm">
                <assert_contents>
                    <not_has_text text="Phosphosite" />
                    <has_text text="cds.comp41779_c0_seq1" />
                </assert_contents>
            </output>
            <output name="output_psm_phosphorylation">
                <assert_contents>
                    <has_text text="Phosphosite" />
                    <has_text text="cds.comp41779_c0_seq1" />
                </assert_contents>
            </output>
            <output name="output_peptides">
                <assert_contents>
                    <has_text text="Modification" />
                    <has_text text="cds.comp41779_c0_seq1" />
                </assert_contents>
            </output>
            <output name="output_peptides_phosphorylation">
                <assert_contents>
                    <has_text text="Phosphosite" />
                    <has_text text="cds.comp41779_c0_seq1" />
                </assert_contents>
            </output>
            <output name="output_proteins">
                <assert_contents>
                    <has_text text="Modification" />
                    <has_text text="cds.comp41779_c0_seq1" />
                </assert_contents>
            </output>
            <output name="output_proteins_phosphorylation">
                <assert_contents>
                    <has_text text="Phosphosite" />
                    <has_text text="cds.comp41779_c0_seq1" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
**What it does**

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

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

----

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: Number of Confident Modification Sites	List of the sites where a variable modification was confidently localized.
* Other Modification Sites: Number of 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.


Hierachical 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.


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**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>