Mercurial > repos > galaxyp > fragpipe
diff fragpipe.xml @ 7:b4f6df8fa89b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
| author | galaxyp |
|---|---|
| date | Wed, 01 Oct 2025 22:20:54 +0000 |
| parents | 59fec1e2a6c3 |
| children | 1455d3e7f191 |
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--- a/fragpipe.xml Sun Mar 30 23:00:45 2025 +0000 +++ b/fragpipe.xml Wed Oct 01 22:20:54 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="fragpipe" name="FragPipe - Academic Research and Education User License (Non-Commercial)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> +<tool id="fragpipe" name="FragPipe - Academic Research and Education User License (Non-Commercial)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2"> <description>Data analysis for mass spectrometry-based proteomics</description> <macros> <import>macros.xml</import> @@ -12,8 +12,9 @@ level="fatal" description="A FragPipe pipeline process returned non-zero exit code."/> </stdio> - - <version_command>fragpipe --help | grep 'FragPipe v'</version_command> + <version_command> + fragpipe --msfragger_key @MSFRAGGER_ACADEMIC_USE_KEY@ --ionquant_key @IONQUANT_ACADEMIC_USE_KEY@ --help | grep 'FragPipe v' + </version_command> <!-- FragPipe wrapper command: @@ -32,19 +33,24 @@ @PREPARE_INPUTS@ @PREPARE_DATABASE@ + mkdir tools && + ln -s \${env_location}/share/diatracer-*/diaTracer-*/diaTracer-*.jar tools/ && + ln -s \${env_location}/share/ionquant-*/IonQuant-*/IonQuant-*.jar tools/ && + ln -s \${env_location}/share/msfragger-*/MSFragger-*/MSFragger-*.jar tools/ && + ln -s \${env_location}/share/msfragger-*/MSFragger-*/ext tools/ && + ## Run FragPipe '$__tool_directory__/fragpipe' - --msfragger_key f28c4be2-759b0a11-6c1ea652-1240565a - --ionquant_key 47cb2953-b4bf7726-2c96f5fe-8f1013aa + --msfragger_key @MSFRAGGER_ACADEMIC_USE_KEY@ + --ionquant_key @IONQUANT_ACADEMIC_USE_KEY@ + --diatracer_key @DIATRACER_ACADEMIC_USE_KEY@ --headless --threads \${GALAXY_SLOTS:-8} --ram \$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ] --workflow fp.workflow --manifest fp.manifest --workdir outputs - --config-msfragger \${env_location}/share/msfragger-*/MSFragger-*/MSFragger-*.jar - --config-philosopher \$(which philosopher) - --config-python \$(which python) - --config-ionquant \${env_location}/share/ionquant-*/IonQuant.jar && + --config-tools-folder tools + --config-python \$(which python) && @PREPARE_OUTPUTS@ #end if @@ -76,65 +82,96 @@ <option value="log">FragPipe Log</option> <option value="combined_outputs">FragPipe Combined Outputs</option> <option value="concatenated_outputs">TSV Outputs Concatenated</option> + <option value="individual_outputs">Individual Experiment Outputs</option> </param> </inputs> <outputs> <!-- Workflow file used by FragPipe --> - <data name="output_workflow" format="txt" label="${tool.name} on ${on_string}: workflow" from_work_dir="fp.workflow"> + <data name="output_workflow" format="txt" label="FragPipe workflow" from_work_dir="fp.workflow"> <filter>workflow_only or (output_options and 'workflow' in output_options)</filter> </data> <!-- FragPipe log --> - <data name="log" format="txt" label="${tool.name} on ${on_string}: log.txt" from_work_dir="outputs/log_*.txt"> + <data name="log" format="txt" label="FragPipe log.txt" from_work_dir="outputs/log_*.txt"> <filter>not workflow_only and output_options and 'log' in output_options</filter> </data> + <!-- DIA-NN Quant --> + <data name="diaquant_msstats_csv" format="csv" label="FragPipe DIA-NN Quant msstats.csv" from_work_dir="outputs/dia-quant-output/msstats.csv"> + <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter> + </data> + <data name="diaquant_msstats_ptm_csv" format="csv" label="FragPipe DIA-NN Quant msstats_ptm.csv" from_work_dir="outputs/dia-quant-output/msstats_ptm.csv"> + <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter> + </data> + <data name="diaquant_report_tsv_speclib" format="txt" label="FragPipe DIA-NN Quant report-tsv.speclib" from_work_dir="outputs/dia-quant-output/report-tsv.speclib"> + <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter> + </data> + <data name="diaquant_report_gg_matrix_tsv" format="tsv" label="FragPipe DIA-NN Quant report.gg_matrix.tsv" from_work_dir="outputs/dia-quant-output/report.gg_matrix.tsv"> + <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter> + </data> + <data name="diaquant_report_log_txt" format="txt" label="FragPipe DIA-NN Quant report.log.txt" from_work_dir="outputs/dia-quant-output/report.log.txt"> + <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter> + </data> + <data name="diaquant_report_pg_matrix_tsv" format="tsv" label="FragPipe DIA-NN Quant report.pg_matrix.tsv" from_work_dir="outputs/dia-quant-output/report.pg_matrix.tsv"> + <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter> + </data> + <data name="diaquant_report_pr_matrix_tsv" format="tsv" label="FragPipe DIA-NN Quant report.pr_matrix.tsv" from_work_dir="outputs/dia-quant-output/report.pr_matrix.tsv"> + <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter> + </data> + <data name="diaquant_report_stats_tsv" format="tsv" label="FragPipe DIA-NN Quant report.stats.tsv" from_work_dir="outputs/dia-quant-output/report.stats.tsv"> + <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter> + </data> + <data name="diaquant_report_tsv" format="tsv" label="FragPipe DIA-NN Quant report.tsv" from_work_dir="outputs/dia-quant-output/report.tsv"> + <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter> + </data> + <data name="diaquant_report_unique_genes_matrix_tsv" format="tsv" label="FragPipe DIA-NN Quant report.unique_genes_matrix.tsv" from_work_dir="outputs/dia-quant-output/report.unique_genes_matrix.tsv"> + <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter> + </data> + + <!-- Collection outputs comprised of separate results for different experiments --> - <collection name="output_psm" type="list" label="${tool.name} - ${on_string}: psm.tsv" > - <filter>not workflow_only</filter> + <collection name="output_psm" type="list" label="FragPipe psm.tsv" > + <filter>not workflow_only and 'individual_outputs' in output_options</filter> <discover_datasets pattern="(?P<designation>.+\.psm.tsv)" ext="tabular" directory="outputs"/> </collection> - <collection name="output_ion" type="list" label="${tool.name} - ${on_string}: ion.tsv" > - <filter>not workflow_only</filter> + <collection name="output_ion" type="list" label="FragPipe ion.tsv" > + <filter>not workflow_only and 'individual_outputs' in output_options</filter> <discover_datasets pattern="(?P<designation>.+\.ion.tsv)" ext="tabular" directory="outputs"/> </collection> - <collection name="output_peptide" type="list" label="${tool.name} - ${on_string}: peptide.tsv" > - <filter>not workflow_only</filter> + <collection name="output_peptide" type="list" label="FragPipe peptide.tsv" > + <filter>not workflow_only and 'individual_outputs' in output_options</filter> <discover_datasets pattern="(?P<designation>.+\.peptide.tsv)" ext="tabular" directory="outputs"/> </collection> - <collection name="output_protein" type="list" label="${tool.name} - ${on_string}: protein.tsv" > - <filter>not workflow_only</filter> + <collection name="output_protein" type="list" label="FragPipe protein.tsv" > + <filter>not workflow_only and 'individual_outputs' in output_options</filter> <discover_datasets pattern="(?P<designation>.+\.protein.tsv)" ext="tabular" directory="outputs"/> </collection> <!-- Combined results from all experimental groups --> - <collection name="combined_outputs" type="list" label="${tool.name} - ${on_string}: Combined Outputs" > + <collection name="combined_outputs" type="list" label="FragPipe Combined Outputs" > <filter>not workflow_only and output_options and 'combined_outputs' in output_options</filter> <discover_datasets pattern="__designation__" ext="tabular" directory="outputs/combined_outputs"/> </collection> <!-- Galaxy-wrapper concatenated results --> - <data name="concat_psm_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated psm.tsv" from_work_dir="outputs/concat_psm.tsv"> + <data name="concat_psm_tsv" format="tabular" label="FragPipe Concatenated psm.tsv" from_work_dir="outputs/concat_psm.tsv"> <filter>not workflow_only and 'concatenated_outputs' in output_options</filter> </data> - <data name="concat_ion_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated ion.tsv" from_work_dir="outputs/concat_ion.tsv"> + <data name="concat_ion_tsv" format="tabular" label="FragPipe Concatenated ion.tsv" from_work_dir="outputs/concat_ion.tsv"> <filter>not workflow_only and 'concatenated_outputs' in output_options</filter> </data> - <data name="concat_peptide_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated peptide.tsv" from_work_dir="outputs/concat_peptide.tsv"> + <data name="concat_peptide_tsv" format="tabular" label="FragPipe Concatenated peptide.tsv" from_work_dir="outputs/concat_peptide.tsv"> <filter>not workflow_only and 'concatenated_outputs' in output_options</filter> </data> - <data name="concat_protein_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated protein.tsv" from_work_dir="outputs/concat_protein.tsv"> + <data name="concat_protein_tsv" format="tabular" label="FragPipe Concatenated protein.tsv" from_work_dir="outputs/concat_protein.tsv"> <filter>not workflow_only and 'concatenated_outputs' in output_options</filter> </data> <!-- PTM-Shepherd Results --> - <data name="global_profile_tsv" format="tabular" label="${tool.name} on ${on_string}: global.profile.tsv" from_work_dir="outputs/global.profile.tsv"> + <data name="global_profile_tsv" format="tabular" label="FragPipe global.profile.tsv" from_work_dir="outputs/ptm-shepherd-output/global.profile.tsv"> <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter> </data> - <data name="global_summary_tsv" format="tabular" label="${tool.name} on ${on_string}: global.modsummary.tsv" from_work_dir="outputs/global.modsummary.tsv"> - <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter> - </data> - <data name="global_diagmine_tsv" format="tabular" label="${tool.name} on ${on_string}: global.diagmine.tsv" from_work_dir="outputs/global.diagmine.tsv"> + <data name="global_summary_tsv" format="tabular" label="FragPipe global.modsummary.tsv" from_work_dir="outputs/ptm-shepherd-output/global.modsummary.tsv"> <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter> </data> @@ -142,7 +179,7 @@ TMT/iTRAW Results Only produced by TMT, TRAQ, and SLC workflows --> - <collection name="tmt_results" type="list" label="${tool.name} - ${on_string}: TMT Results" > + <collection name="tmt_results" type="list" label="FragPipe TMT Results" > <discover_datasets pattern="__designation__" ext="tabular" directory="outputs/tmt-report"/> <filter>(not workflow_only) and ('TMT' in wf['workflow_name'])</filter> </collection> @@ -150,67 +187,63 @@ <tests> <test expect_num_outputs="11"> - <param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/> - <param name="database_name" value="default/test.fasta" ftype="fasta"/> - <param name="manifest" value="default/test.manifest" ftype="tabular"/> - <param name="wf|workflow_name" value="Default"/> - <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/> + <param name="inputs" value="basic-search/test1.mzML,basic-search/test2.mzML" ftype="mzml"/> + <param name="database_name" value="basic-search/test.fasta" ftype="fasta"/> + <param name="manifest" value="basic-search/test.manifest" ftype="tabular"/> + <param name="wf|workflow_name" value="Basic-Search"/> + <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs,individual_outputs"/> <param name="license_agreements" value="true"/> <param name="wf|validation|validation_tab|psm_validation|run_psm_validation" value="percolator"/> <output name="concat_psm_tsv" ftype="tabular"> <assert_contents> - <has_text text="Experiment	Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> + <has_text text="Experiment	Spectrum	Spectrum File"/> <has_text text="sample1"/> + <has_text text="sample2"/> </assert_contents> </output> <output name="concat_ion_tsv" ftype="tabular"> <assert_contents> - <has_text text="Experiment	Peptide Sequence	Modified Sequence	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	M/Z	Charge	Observed Mass	Probability	Expectation	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> + <has_text text="Experiment	Peptide Sequence	Modified Sequence"/> <has_text text="sample1"/> + <has_text text="sample2"/> </assert_contents> </output> <output name="concat_peptide_tsv" ftype="tabular"> <assert_contents> - <has_text text="Experiment	Peptide	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	Charges	Probability	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> + <has_text text="Experiment	Peptide	Prev AA	"/> <has_text text="sample1"/> + <has_text text="sample2"/> </assert_contents> </output> <output name="concat_protein_tsv" ftype="tabular"> <assert_contents> - <has_text text="Experiment	Protein	Protein ID	Entry Name	Gene	Length	Organism	Protein Description	Protein Existence	Coverage	Protein Probability	Top Peptide Probability	Total Peptides	Unique Peptides	Razor Peptides	Total Spectral Count	Unique Spectral Count	Razor Spectral Count	Total Intensity	Unique Intensity	Razor Intensity	Razor Assigned Modifications	Razor Observed Modifications	Indistinguishable Proteins"/> + <has_text text="Experiment	Protein	Protein ID	"/> <has_text text="sample1"/> + <has_text text="sample2"/> </assert_contents> </output> - <output name="output_workflow" ftype="txt" file="default/outputs/workflow.txt" compare="contains"> - <assert_contents> - <has_text text="crystalc.run-crystalc=false"/> - </assert_contents> - </output> + <output name="output_workflow" ftype="txt" file="basic-search/outputs/workflow.txt" compare="contains"/> <output name="log" ftype="txt"> <assert_contents> - <has_text text="FragPipe version 20.0"/> + <has_text text="FragPipe version 23.0"/> </assert_contents> </output> <output_collection name="combined_outputs" type="list"> <element name="combined_protein.tsv" ftype="tabular"> <assert_contents> - <has_text text="Protein	Protein ID	Entry Name	Gene	Protein Length	Organism	Protein Existence	Description	Protein Probability	Top Peptide Probability	Combined Total Peptides	Combined Spectral Count	Combined Unique Spectral Count	Combined Total Spectral Count	sample1 Spectral Count	sample2 Spectral Count	sample1 Intensity	sample2 Intensity	Indistinguishable Proteins"/> + <has_text text="Protein	Protein ID	Entry Name"/> </assert_contents> </element> </output_collection> </test> - <test expect_num_outputs="11"> - <param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/> - <param name="database_name" value="default/test.fasta" ftype="fasta"/> - <param name="manifest" value="default/test.manifest" ftype="tabular"/> + <test expect_num_outputs="7"> + <param name="inputs" value="basic-search/test1.mzML,basic-search/test2.mzML" ftype="mzml"/> + <param name="database_name" value="basic-search/test.fasta" ftype="fasta"/> + <param name="manifest" value="basic-search/test.manifest" ftype="tabular"/> <param name="wf|workflow_name" value="Nonspecific-HLA"/> <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/> <param name="license_agreements" value="true"/> - <output name="output_workflow" ftype="txt" file="nonspecific-hla/outputs/workflow.txt" compare="contains"> - <assert_contents> - <has_text text="crystalc.run-crystalc=false"/> - </assert_contents> - </output> + <output name="output_workflow" ftype="txt" file="nonspecific-hla/outputs/workflow.txt" compare="contains"/> <output name="concat_protein_tsv" ftype="tabular"> <assert_contents> <has_text text="sample1"/> @@ -219,110 +252,16 @@ </assert_contents> </output> </test> - <test expect_num_outputs="11"> - <param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/> - <param name="database_name" value="default/test.fasta" ftype="fasta"/> - <param name="manifest" value="default/test.manifest" ftype="tabular"/> - <param name="wf|workflow_name" value="Default"/> - <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/> - <param name="license_agreements" value="true"/> - <param name="wf|validation|validation_tab|psm_validation|run_psm_validation" value="msbooster_percolator"/> - <output name="concat_psm_tsv" ftype="tabular"> - <assert_contents> - <has_text text="Experiment	Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	SpectralSim	RTScore	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> - <has_text text="sample1"/> - </assert_contents> - </output> - <output name="concat_ion_tsv" ftype="tabular"> - <assert_contents> - <has_text text="Experiment	Peptide Sequence	Modified Sequence	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	M/Z	Charge	Observed Mass	Probability	Expectation	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> - <has_text text="sample1"/> - </assert_contents> - </output> - <output name="concat_peptide_tsv" ftype="tabular"> - <assert_contents> - <has_text text="Experiment	Peptide	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	Charges	Probability	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> - <has_text text="sample1"/> - </assert_contents> - </output> - <output name="concat_protein_tsv" ftype="tabular"> - <assert_contents> - <has_text text="Experiment	Protein	Protein ID	Entry Name	Gene	Length	Organism	Protein Description	Protein Existence	Coverage	Protein Probability	Top Peptide Probability	Total Peptides	Unique Peptides	Razor Peptides	Total Spectral Count	Unique Spectral Count	Razor Spectral Count	Total Intensity	Unique Intensity	Razor Intensity	Razor Assigned Modifications	Razor Observed Modifications	Indistinguishable Proteins"/> - <has_text text="sample1"/> - </assert_contents> - </output> - <output name="output_workflow" ftype="txt" file="default/outputs/workflow_msbooster_percolator.txt" compare="contains"> - <assert_contents> - <has_text text="crystalc.run-crystalc=false"/> - </assert_contents> - </output> - <output name="log" ftype="txt"> - <assert_contents> - <has_text text="FragPipe version 20.0"/> - </assert_contents> - </output> - <output_collection name="combined_outputs" type="list"> - <element name="combined_protein.tsv" ftype="tabular"> - <assert_contents> - <has_text text="Protein	Protein ID	Entry Name	Gene	Protein Length	Organism	Protein Existence	Description	Protein Probability	Top Peptide Probability	Combined Total Peptides	Combined Spectral Count	Combined Unique Spectral Count	Combined Total Spectral Count	sample1 Spectral Count	sample2 Spectral Count	sample1 Intensity	sample2 Intensity	Indistinguishable Proteins"/> - </assert_contents> - </element> - </output_collection> - </test> - <test expect_num_outputs="11"> + <test expect_num_outputs="1"> <param name="inputs" value="tmt11/test1.mzML,tmt11/test2.mzML" ftype="mzml"/> <param name="database_name" value="tmt11/test.fasta" ftype="fasta"/> <param name="manifest" value="tmt11/test.manifest" ftype="tabular"/> <param name="wf|annotation" value="tmt11/test.annotation" ftype="tabular"/> <param name="wf|workflow_name" value="TMT11"/> - <param name="output_options" value="workflow,log,concatenated_outputs"/> + <param name="output_options" value="workflow"/> <param name="license_agreements" value="true"/> - <output name="concat_psm_tsv" ftype="tabular"> - <assert_contents> - <has_text text="Experiment	Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	SpectralSim	RTScore	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> - <has_text text="sample1"/> - </assert_contents> - </output> - <output name="concat_ion_tsv" ftype="tabular"> - <assert_contents> - <has_text text="Experiment	Peptide Sequence	Modified Sequence	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	M/Z	Charge	Observed Mass	Probability	Expectation	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> - <has_text text="sample1"/> - </assert_contents> - </output> - <output name="concat_peptide_tsv" ftype="tabular"> - <assert_contents> - <has_text text="Experiment	Peptide	Prev AA	Next AA	Peptide Length	Protein Start	Protein End	Charges	Probability	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins"/> - <has_text text="sample1"/> - </assert_contents> - </output> - <output name="concat_protein_tsv" ftype="tabular"> - <assert_contents> - <has_text text="Experiment	Protein	Protein ID	Entry Name	Gene	Length	Organism	Protein Description	Protein Existence	Coverage	Protein Probability	Top Peptide Probability	Total Peptides	Unique Peptides	Razor Peptides	Total Spectral Count	Unique Spectral Count	Razor Spectral Count	Total Intensity	Unique Intensity	Razor Intensity	Razor Assigned Modifications	Razor Observed Modifications	Indistinguishable Proteins"/> - <has_text text="sample1"/> - </assert_contents> - </output> - <output name="output_workflow" ftype="txt" file="tmt11/outputs/workflow.txt" compare="contains"> - <assert_contents> - <has_text text="crystalc.run-crystalc=false"/> - </assert_contents> - </output> - <output name="log" ftype="txt"> - <assert_contents> - <has_text text="FragPipe version 20.0"/> - </assert_contents> - </output> - <output_collection name="tmt_results" type="list"> - <element name="abundance_gene_MD.tsv" ftype="tabular"> - <assert_contents> - <has_text text="Index	NumberPSM	ProteinID	MaxPepProb	ReferenceIntensity	sample-01	sample-02	sample-03	sample-04	sample-05	sample-06	sample-07	sample-08	sample-09	sample-10	Bridge"/> - </assert_contents> - </element> - <element name="ratio_gene_MD.tsv" ftype="tabular"> - <assert_contents> - <has_text text="Index	NumberPSM	ProteinID	MaxPepProb	ReferenceIntensity	sample-01	sample-02	sample-03	sample-04	sample-05	sample-06	sample-07	sample-08	sample-09	sample-10	Bridge"/> - </assert_contents> - </element> - </output_collection> + <param name="workflow_only" value="true"/> + <output name="output_workflow" ftype="txt" file="tmt11/outputs/workflow.txt" compare="contains"/> </test> </tests> @@ -332,7 +271,8 @@ FragPipe_ is a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. FragPipe uses MSFragger_ - an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification. -FragPipe_ runs a user selected analysis workflow_ +Each FragPipe job is configured around a user-selected FragPipe _workflow. +Blank optional parameters in the Galaxy tool will default to the settings in the selected FragPipe workflow file. **License Agreements**