| Previous changeset 3:da9ebef968bd (2024-09-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43 |
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modified:
fragpipe.xml macros.xml |
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added:
test-data/default/outputs/workflow_msbooster_percolator.txt |
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| diff -r da9ebef968bd -r e969a182e3cb fragpipe.xml --- a/fragpipe.xml Thu Sep 12 08:06:44 2024 +0000 +++ b/fragpipe.xml Fri Dec 13 15:17:28 2024 +0000 |
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| @@ -200,6 +200,57 @@ </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"/> + <param name="workflow_name" value="Default"/> + <param name="label_free_quantification_run" value="ionquant"/> + <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/> + <param name="license_agreements" value="true"/> + <param name="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"> <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"/> |
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| diff -r da9ebef968bd -r e969a182e3cb macros.xml --- a/macros.xml Thu Sep 12 08:06:44 2024 +0000 +++ b/macros.xml Fri Dec 13 15:17:28 2024 +0000 |
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| @@ -1,7 +1,7 @@ <macros> <import>msfragger_macros.xml</import> <token name="@TOOL_VERSION@">20.0</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX@">4</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement> @@ -350,13 +350,27 @@ <!-- Set Percolator workflow options --> <token name="@PERCOLATOR@"><![CDATA[ #set $prc = $wf.validation.validation_tab.psm_validation.percolator - #set $wfdict['run-validation-tab'] = $wf.validation.validation_tab.run_validation - #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false' #set $wfdict['percolator.run-percolator'] = 'true' #set $wfdict['percolator.keep-tsv-files'] = str($prc.keep_tsv_files) #set $wfdict['percolator.min-prob'] = str($prc.min_prob) ]]></token> + <xml name="msbooster"> + <section name="msbooster" expanded="true" title="MSBooster"> + <param name="predict_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict RT"/> + <param name="predict_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict spectra"/> + <param name="use_correlated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use correlated features"/> + </section> + </xml> + <token name="@MSBOOSTER@"><![CDATA[ + #set $prfx = $wf.validation.validation_tab.psm_validation.msbooster + #set $wfdict['msbooster.run-msbooster'] = 'true' + #set $wfdict['msbooster.predict-rt'] = str($prfx.predict_rt) + #set $wfdict['msbooster.predict-spectra'] = str($prfx.predict_spectra) + #set $wfdict['msbooster.use-correlated-features'] = str($prfx.use_correlated_features) + ]]></token> + + <!-- Philosopher Report (phi-report) options --> <xml name="phi_report"> <conditional name="phi_report"> @@ -424,16 +438,6 @@ <param name="run_crystalc" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Run Crystal-C" help="Recommend for open searches for additional resuts cleanup"/> </xml> - <!-- MSBooster options. Disabled until DIA-NN integrated. - <xml name="msbooster"> - <section name="msbooster" expanded="false" title="MSBooster"> - <param name="predict_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict RT"/> - <param name="predict_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict spectra"/> - <param name="use_correlated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use correlated features"/> - </section> - </xml> - --> - <!-- Protein Prophet options --> <xml name="protein_prophet" token_minprob="0.05"> <conditional name="protein_prophet"> @@ -484,9 +488,7 @@ <param name="run_psm_validation" type="select" label="PSM Validation"> <option value="peptide_prophet" selected="@PEP@">Run PeptideProphet</option> <option value="percolator" selected="@PERC@">Run Percolator</option> - <!-- MSBooster disabled until DIA-NN integrated <option value="msbooster_percolator" selected="@BOOST@">Run MSBooster and Percolator</option> - --> <option value="no" selected="@NO@">Use workflow values</option> </param> <when value="peptide_prophet"> @@ -495,12 +497,10 @@ <when value="percolator"> <expand macro="percolator"/> </when> - <!-- MSBooster disabled until DIA-NN integrated <when value="msbooster_percolator"> <expand macro="msbooster"/> <expand macro="percolator"/> </when> - --> <when value="no"> </when> </conditional> @@ -524,9 +524,13 @@ #elif $prfx.run_psm_validation == 'percolator' #set $wfdict['run-psm-validation'] = 'true' #set $wfdict['msbooster.run-msbooster'] = 'false' + #set $wfdict['peptide-prophet.run-peptide-prophet=false'] = 'false' @PERCOLATOR@ - ##elif $prfx.run_psm_validation == 'msbooster_percolator' - # MSBooster disabled until DIA-NN integrated. + #elif $prfx.run_psm_validation == 'msbooster_percolator' + #set $wfdict['run-psm-validation'] = 'true' + #set $wfdict['peptide-prophet.run-peptide-prophet=false'] = 'false' + @MSBOOSTER@ + @PERCOLATOR@ #end if @PROTEINPROPHET@ @PHIREPORT@ |
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| diff -r da9ebef968bd -r e969a182e3cb test-data/default/outputs/workflow_msbooster_percolator.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/default/outputs/workflow_msbooster_percolator.txt Fri Dec 13 15:17:28 2024 +0000 |
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| b'@@ -0,0 +1,308 @@\n+database.decoy-tag=rev_\n+diann.fragpipe.cmd-opts=\n+diann.heavy=\n+diann.library=\n+diann.light=\n+diann.medium=\n+diann.q-value=0.01\n+diann.quantification-strategy=3\n+diann.run-dia-nn=false\n+diann.run-dia-plex=false\n+diann.run-specific-protein-q-value=false\n+diann.unrelated-runs=false\n+diann.use-predicted-spectra=true\n+diaumpire.AdjustFragIntensity=true\n+diaumpire.BoostComplementaryIon=false\n+diaumpire.CorrThreshold=0\n+diaumpire.DeltaApex=0.2\n+diaumpire.ExportPrecursorPeak=false\n+diaumpire.Q1=true\n+diaumpire.Q2=true\n+diaumpire.Q3=true\n+diaumpire.RFmax=500\n+diaumpire.RPmax=25\n+diaumpire.RTOverlap=0.3\n+diaumpire.SE.EstimateBG=false\n+diaumpire.SE.IsoPattern=0.3\n+diaumpire.SE.MS1PPM=10\n+diaumpire.SE.MS2PPM=20\n+diaumpire.SE.MS2SN=1.1\n+diaumpire.SE.MassDefectFilter=true\n+diaumpire.SE.MassDefectOffset=0.1\n+diaumpire.SE.NoMissedScan=1\n+diaumpire.SE.SN=1.1\n+diaumpire.run-diaumpire=false\n+freequant.mz-tol=10\n+freequant.rt-tol=0.4\n+freequant.run-freequant=false\n+ionquant.excludemods=\n+ionquant.heavy=\n+ionquant.imtol=0.05\n+ionquant.ionfdr=0.01\n+ionquant.light=\n+ionquant.locprob=0.75\n+ionquant.maxlfq=1\n+ionquant.mbr=1\n+ionquant.mbrimtol=0.05\n+ionquant.mbrmincorr=0\n+ionquant.mbrrttol=1\n+ionquant.mbrtoprun=10\n+ionquant.medium=\n+ionquant.minfreq=0\n+ionquant.minions=2\n+ionquant.minisotopes=2\n+ionquant.minscans=3\n+ionquant.mztol=10\n+ionquant.normalization=1\n+ionquant.peptidefdr=1\n+ionquant.proteinfdr=1\n+ionquant.requantify=1\n+ionquant.rttol=0.4\n+ionquant.run-ionquant=true\n+ionquant.tp=0\n+ionquant.uniqueness=0\n+ionquant.use-labeling=false\n+ionquant.use-lfq=true\n+ionquant.writeindex=0\n+msbooster.predict-rt=true\n+msbooster.predict-spectra=true\n+msbooster.run-msbooster=true\n+msbooster.use-correlated-features=false\n+msfragger.Y_type_masses=\n+msfragger.activation_types=all\n+msfragger.add_topN_complementary=0\n+msfragger.allowed_missed_cleavage_1=2\n+msfragger.allowed_missed_cleavage_2=2\n+msfragger.calibrate_mass=2\n+msfragger.check_spectral_files=true\n+msfragger.clip_nTerm_M=true\n+msfragger.deisotope=1\n+msfragger.delta_mass_exclude_ranges=(-1.5,3.5)\n+msfragger.deneutralloss=1\n+msfragger.diagnostic_fragments=\n+msfragger.diagnostic_intensity_filter=0\n+msfragger.digest_max_length=50\n+msfragger.digest_min_length=7\n+msfragger.fragment_ion_series=b,y\n+msfragger.fragment_mass_tolerance=20\n+msfragger.fragment_mass_units=1\n+msfragger.group_variable=0\n+msfragger.intensity_transform=0\n+msfragger.ion_series_definitions=\n+msfragger.isotope_error=0/1/2/3\n+msfragger.labile_search_mode=off\n+msfragger.localize_delta_mass=false\n+msfragger.mass_diff_to_variable_mod=0\n+msfragger.mass_offsets=0\n+msfragger.max_fragment_charge=2\n+msfragger.max_variable_mods_combinations=5000\n+msfragger.max_variable_mods_per_peptide=3\n+msfragger.min_fragments_modelling=2\n+msfragger.min_matched_fragments=4\n+msfragger.min_sequence_matches=2\n+msfragger.minimum_peaks=15\n+msfragger.minimum_ratio=0.01\n+msfragger.misc.fragger.clear-mz-hi=0.0\n+msfragger.misc.fragger.clear-mz-lo=0.0\n+msfragger.misc.fragger.digest-mass-hi=5000\n+msfragger.misc.fragger.digest-mass-lo=500\n+msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin\n+msfragger.misc.fragger.enzyme-dropdown-2=null\n+msfragger.misc.fragger.precursor-charge-hi=4\n+msfragger.misc.fragger.precursor-charge-lo=1\n+msfragger.misc.fragger.remove-precursor-range-hi=1.5\n+msfragger.misc.fragger.remove-precursor-range-lo=-1.5\n+msfragger.misc.slice-db=1\n+msfragger.num_enzyme_termini=2\n+msfragger.output_format=pepXML_pin\n+msfragger.output_max_expect=50.0\n+msfragger.output_report_topN=1\n+msfragger.output_report_topN_dia1=5\n+msfragger.output_report_topN_dia2=3\n+msfragger.override_charge=false\n+msfragger.precursor_mass_lower=-20\n+msfragger.precursor_mass_mode=selected\n+msfragger.precursor_mass_units=1\n+msfragger.precursor_mass_upper=20\n+msfragger.precursor_true_tolerance=20\n+msfragger.precursor_true_units=1\n+msfragger.remainder_fragment_masses=\n+msfragger.remove_precursor_peak=1\n+msfragger.report_alternative_proteins=true\n+msfragger.require_precursor='..b'1\n+ptmshepherd.cap_y_ions=\n+ptmshepherd.decoy_type=1\n+ptmshepherd.diag_ions=\n+ptmshepherd.diagextract_mode=false\n+ptmshepherd.diagmine_diagMinFoldChange=3.0\n+ptmshepherd.diagmine_diagMinSpecDiff=00.2\n+ptmshepherd.diagmine_fragMinFoldChange=3.0\n+ptmshepherd.diagmine_fragMinPropensity=00.1\n+ptmshepherd.diagmine_fragMinSpecDiff=00.1\n+ptmshepherd.diagmine_minIonsPerSpec=2\n+ptmshepherd.diagmine_minPeps=25\n+ptmshepherd.diagmine_mode=false\n+ptmshepherd.diagmine_pepMinFoldChange=3.0\n+ptmshepherd.diagmine_pepMinSpecDiff=00.2\n+ptmshepherd.glyco_adducts=\n+ptmshepherd.glyco_fdr=1.00\n+ptmshepherd.glyco_isotope_max=3\n+ptmshepherd.glyco_isotope_min=-1\n+ptmshepherd.glyco_mode=false\n+ptmshepherd.glyco_ppm_tol=50\n+ptmshepherd.glycodatabase=\n+ptmshepherd.histo_smoothbins=2\n+ptmshepherd.iontype_a=false\n+ptmshepherd.iontype_b=true\n+ptmshepherd.iontype_c=true\n+ptmshepherd.iontype_x=false\n+ptmshepherd.iontype_y=true\n+ptmshepherd.iontype_z=true\n+ptmshepherd.localization_allowed_res=\n+ptmshepherd.localization_background=4\n+ptmshepherd.max_adducts=0\n+ptmshepherd.n_glyco=true\n+ptmshepherd.normalization-psms=true\n+ptmshepherd.normalization-scans=false\n+ptmshepherd.output_extended=false\n+ptmshepherd.peakpicking_mass_units=0\n+ptmshepherd.peakpicking_minPsm=10\n+ptmshepherd.peakpicking_promRatio=0.3\n+ptmshepherd.peakpicking_width=0.002\n+ptmshepherd.precursor_mass_units=0\n+ptmshepherd.precursor_tol=0.01\n+ptmshepherd.print_decoys=false\n+ptmshepherd.prob_dhexOx=2,0.5,0.1\n+ptmshepherd.prob_dhexY=2,0.5\n+ptmshepherd.prob_neuacOx=2,0.05,0.2\n+ptmshepherd.prob_neugcOx=2,0.05,0.2\n+ptmshepherd.prob_phosphoOx=2,0.05,0.2\n+ptmshepherd.prob_regY=5,0.5\n+ptmshepherd.prob_sulfoOx=2,0.05,0.2\n+ptmshepherd.remainder_masses=\n+ptmshepherd.remove_glycan_delta_mass=true\n+ptmshepherd.run-shepherd=false\n+ptmshepherd.spectra_maxfragcharge=2\n+ptmshepherd.spectra_ppmtol=20\n+ptmshepherd.varmod_masses=\n+quantitation.run-label-free-quant=false\n+run-psm-validation=true\n+run-validation-tab=true\n+saintexpress.fragpipe.cmd-opts=\n+saintexpress.max-replicates=10\n+saintexpress.run-saint-express=false\n+saintexpress.virtual-controls=100\n+speclibgen.easypqp.extras.max_delta_ppm=15\n+speclibgen.easypqp.extras.max_delta_unimod=0.02\n+speclibgen.easypqp.extras.rt_lowess_fraction=0\n+speclibgen.easypqp.fragment.a=false\n+speclibgen.easypqp.fragment.b=true\n+speclibgen.easypqp.fragment.c=false\n+speclibgen.easypqp.fragment.x=false\n+speclibgen.easypqp.fragment.y=true\n+speclibgen.easypqp.fragment.z=false\n+speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM\n+speclibgen.easypqp.neutral_loss=false\n+speclibgen.easypqp.rt-cal=ciRT\n+speclibgen.easypqp.select-file.text=\n+speclibgen.easypqp.select-im-file.text=\n+speclibgen.keep-intermediate-files=false\n+speclibgen.run-speclibgen=false\n+tab-run.delete_calibrated_mzml=false\n+tab-run.delete_temp_files=false\n+tab-run.sub_mzml_prob_threshold=0.5\n+tab-run.write_sub_mzml=false\n+tmtintegrator.add_Ref=-1\n+tmtintegrator.aggregation_method=0\n+tmtintegrator.allow_overlabel=true\n+tmtintegrator.allow_unlabeled=true\n+tmtintegrator.best_psm=true\n+tmtintegrator.channel_num=TMT-6\n+tmtintegrator.dont-run-fq-lq=false\n+tmtintegrator.glyco_qval=-1\n+tmtintegrator.groupby=0\n+tmtintegrator.log2transformed=true\n+tmtintegrator.max_pep_prob_thres=0\n+tmtintegrator.min_ntt=0\n+tmtintegrator.min_pep_prob=0.9\n+tmtintegrator.min_percent=0.05\n+tmtintegrator.min_purity=0.5\n+tmtintegrator.min_site_prob=-1\n+tmtintegrator.mod_tag=none\n+tmtintegrator.ms1_int=true\n+tmtintegrator.outlier_removal=true\n+tmtintegrator.print_RefInt=false\n+tmtintegrator.prot_exclude=none\n+tmtintegrator.prot_norm=0\n+tmtintegrator.psm_norm=false\n+tmtintegrator.quant_level=2\n+tmtintegrator.ref_tag=Bridge\n+tmtintegrator.run-tmtintegrator=false\n+tmtintegrator.tolerance=20\n+tmtintegrator.top3_pep=true\n+tmtintegrator.unique_gene=0\n+tmtintegrator.unique_pep=false\n+tmtintegrator.use_glycan_composition=false\n+workflow.input.data-type.im-ms=false\n+workflow.input.data-type.regular-ms=true\n+workflow.saved-with-ver=20.0-build5\n' |