Mercurial > repos > galaxyp > peptideshaker
diff peptide_shaker.xml @ 42:80ed6522192c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4
| author | galaxyp |
|---|---|
| date | Fri, 12 Oct 2018 08:55:43 -0400 |
| parents | f63401dd6cbb |
| children | f0878264784c |
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--- a/peptide_shaker.xml Thu Sep 27 04:31:22 2018 -0400 +++ b/peptide_shaker.xml Fri Oct 12 08:55:43 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.26"> +<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> @@ -6,11 +6,12 @@ <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="1.16.26">peptide-shaker</requirement> + <requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement> </requirements> <expand macro="stdio" /> - <command> -<![CDATA[ + + <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") @@ -18,16 +19,33 @@ #set $bin_dir = "bin" - mkdir output_reports; - cwd=`pwd`; + 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 $output_reports_list = set() + #end if + ###################### ## PeptideShakerCLI ## ###################### - (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI + (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="\$cwd/${bin_dir}" + -gui 0 -temp_folder \$cwd/PeptideShakerCLI -experiment '$exp_str' -sample '$samp_str' @@ -35,166 +53,123 @@ -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 - #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 $cleaned_list.remove('zip') - #end if - #if len($cleaned_list) > 0 - ## Only numbers are left over. These corresponds to different reports. - -reports #echo ','.join($cleaned_list)# - #end if - + #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 + ##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 - -ptm_alignment "${processing_options.ptm_alignment}" - -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}" - -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" #end if + -ptm_alignment "${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 - ##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}" + ################################## + ## 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 - - 2>> $temp_stderr) - - && - - echo "Running Reports"; + #end if ################################## ## PeptideShaker Report options ## ################################## - - #if 'mzidentML' in str($outputs).split(','): - echo "Generating mzIdentML"; - (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI - --exec_dir="\$cwd/${bin_dir}" - -in \$cwd/peptideshaker_output.zip - -output_file \$cwd/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>> $temp_stderr) - && + ## Generate Reports if the user has selected one of the 11 additional reports + #if len($output_reports_list) > 0 + -out_reports \$cwd/output_reports + -reports #echo ','.join($output_reports_list)# #end if - ## 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(',') ) ): + 2>> $temp_stderr) - (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI - --exec_dir="\$cwd/${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) - && + #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 "$0" "psmx.txt"' {} \; + #end if #end if - ## # ls -l \$cwd/output_reports/* ; - - #if '0' in str($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) - + && cat $temp_stderr 2>&1; ]]> </command> <inputs> @@ -297,60 +272,92 @@ </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> + <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" /> + </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 ${on_string}: mzidentML file"> - <filter>'mzidentML' in outputs</filter> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and mzidentml_conditional['mzidentml_creation'] is True</filter> </data> <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file"> - <filter>'cps' in outputs</filter> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_cps'] is True</filter> </data> <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive"> - <filter>'zip' in outputs</filter> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True</filter> </data> - <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters"> - <filter>'0' in outputs</filter> + <!-- + <data format="tabular" name="reports"> + <discover_datasets pattern="(?P<designation>.+)\.txt" format="tabular" directory="output_reports" visible="true" assign_primary_output="true" /> + </data> + --> + <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters"> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '0' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report"> - <filter>'1' in outputs</filter> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '1' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report"> - <filter>'2' in outputs</filter> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '2' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> - <filter>'3' in outputs</filter> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '3' in exporting_options['output_reports']</filter> + </data> + <data format="tabular" name="output_psm_nonvalidated" from_work_dir="psm_nonvalidated.txt" label="${tool.name} on ${on_string}: PSM Report with non-validated matches"> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '4' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report"> - <filter>'8' in outputs</filter> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '11' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report"> - <filter>'4' in outputs</filter> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '5' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> - <filter>'5' in outputs</filter> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '6' in exporting_options['output_reports']</filter> + </data> + <data format="tabular" name="output_peptides_nonvalidated" from_work_dir="peptides_nonvalidated.txt" label="${tool.name} on ${on_string}: Peptide Report with non-validated matches"> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '7' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report"> - <filter>'6' in outputs</filter> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '8' in exporting_options['output_reports']</filter> </data> <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> - <filter>'7' in outputs</filter> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '9' in exporting_options['output_reports']</filter> + </data> + <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Repor with non-validated matches"> + <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '10' in exporting_options['output_reports']</filter> </data> </outputs> <tests> @@ -358,88 +365,50 @@ <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="outputs" value="zip,3"/> + <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" /> - <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_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="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.comp" /> - </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> + <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="6"/> + <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> <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="outputs" value="3,cps"/> + <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"> - <assert_contents> - <has_text text="cds.comp41779_c0_seq1" /> - </assert_contents> - </output> + <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/> </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. +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 -http://compomics.github.io/projects/searchgui.html ----