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view peptide_shaker.xml @ 54:7fdd9119cc4f draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e17bb5a0e4a22c7376b2e7a70cf690262a44a0c6"
| author | galaxyp |
|---|---|
| date | Thu, 20 Feb 2020 05:51:38 -0500 |
| parents | d67a3c1bfd09 |
| children | bb0130ff73ce |
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<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@.3"> <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="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement> </requirements> <expand macro="stdio" /> <command><![CDATA[ ## When supporting more advanced Galaxy versions: command use_shared_home="false" #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` && export HOME=\$cwd && echo "" > $temp_stderr && ln -s '$searchgui_input' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par && peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="\$cwd/${bin_dir}" -temp_folder \$cwd/PathSettingsCLI -log \$cwd/peptideshaker.log && #if str($exporting_options.output_reports) != "None" #set $output_reports_list = set(str($exporting_options.output_reports).split(',')) #else #set $output_reports_list = set() #end if ###################### ## PeptideShakerCLI ## ###################### (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="\$cwd/${bin_dir}" -gui 0 -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 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip': -zip \$cwd/peptideshaker_output.zip #end if -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 -ptm_alignment "${processing_options.ptm_alignment}" -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}" -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" #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 ################################## ## mzidCLI options ## ################################## #if $exporting_options.mzidentml_conditional.mzidentml_creation == 1: -output_file \$cwd/output.mzid -include_sequences ${exporting_options.mzidentml_conditional.include_sequences} #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 #end if ################################## ## PeptideShaker Report 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 2>> $temp_stderr) ## 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 $exporting_options.zip_conditional.export_reports_when_zip: && unzip \$cwd/peptideshaker_output.zip 'reports/*' -d \$cwd/output_reports #end if #if len($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 #end if && cat $temp_stderr 2>&1; ]]> </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">A-score</option> <option value="1" selected="True">PhosphoRS</option> <option value="2">None</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> <when value="2" /> </conditional> <param name="ptm_sequence_matching_type" type="select" label="The PTM to peptide sequence matching type"> <option value="0">Character Sequence</option> <option value="1" selected="true">Amino Acids</option> <option value="2">Indistinguishable Amino Acids</option> </param> <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> <section name="exporting_options" expanded="true" title="Exporting options"> <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" /> </when> <when value="0" /> </conditional> <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_cps" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports the CPS 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" /> </when> </conditional> <param name="output_reports" type="select" display="checkboxes" multiple="True" optional="true" label="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="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file"> <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['mzidentml_conditional']['mzidentml_creation'] is True</filter> </data> <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file"> <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_cps'] is True</filter> </data> <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive"> <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True</filter> </data> <!-- <data format="tabular" name="reports"> <discover_datasets pattern="(?P<designation>.+)\.txt" format="tabular" directory="output_reports" visible="true" assign_primary_output="true" /> </data> --> <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters"> <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '0' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report"> <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '1' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report"> <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '2' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '3' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_psm_nonvalidated" from_work_dir="psm_nonvalidated.txt" label="${tool.name} on ${on_string}: PSM Report with non-validated matches"> <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '4' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report"> <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '11' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report"> <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '5' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '6' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_peptides_nonvalidated" from_work_dir="peptides_nonvalidated.txt" label="${tool.name} on ${on_string}: Peptide Report with non-validated matches"> <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '7' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report"> <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '8' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '9' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Repor with non-validated matches"> <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '10' in exporting_options['output_reports']</filter> </data> </outputs> <tests> <test expect_num_outputs="1"> <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/> <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="no"/> <param name="mzidentml_creation" value="0"/> <param name="zip_output_boolean" value="zip"/> <param name="export_cps" value="1"/> <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" /> </test> <test expect_num_outputs="12"> <param name="searchgui_input" value="tiny_searchgui_modifications_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="mzidentml_creation" value="0"/> <param name="zip_output_boolean" value="separate"/> <param name="output_reports" value="0,1,2,3,4,5,6,7,8,9,10,11"/> <output name="output_certificate" file="peptide_shaker_modifications_result1.output_certificate" ftype="txt" lines_diff="8"/> <output name="output_hierarchical" file="peptide_shaker_modifications_result1.output_hierarchical" ftype="tabular"/> <output name="output_extended_psm" file="peptide_shaker_modifications_result1.output_extended_psm" ftype="tabular"/> <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/> <output name="output_psm_phosphorylation" file="peptide_shaker_modifications_result1.output_psm_phosphorylation" ftype="tabular"/> <output name="output_psm_nonvalidated" file="peptide_shaker_modifications_result1.output_psm_nonvalidated" ftype="tabular"/> <output name="output_peptides" file="peptide_shaker_modifications_result1.output_peptides" ftype="tabular"/> <output name="output_peptides_phosphorylation" file="peptide_shaker_modifications_result1.output_peptides_phosphorylation" ftype="tabular"/> <output name="output_peptides_nonvalidated" file="peptide_shaker_modifications_result1.output_peptides_nonvalidated" ftype="tabular"/> <output name="output_proteins" file="peptide_shaker_modifications_result1.output_proteins" ftype="tabular"/> <output name="output_proteins_phosphorylation" file="peptide_shaker_modifications_result1.output_proteins_phosphorylation" ftype="tabular"/> <output name="output_proteins_nonvalidated" file="peptide_shaker_modifications_result1.output_proteins_nonvalidated" ftype="tabular"/> </test> <test expect_num_outputs="2"> <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/> <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="no"/> <param name="mzidentml_creation" value="0"/> <param name="zip_output_boolean" value="separate"/> <param name="export_cps" value="1"/> <param name="output_reports" value="3"/> <output name="output_cps" file="peptide_shaker_modifications_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/> <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/> </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 ---- 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. ------ **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>