diff test-data/peptide_shaker_certificate_result2.txt @ 10:9d12b1d3c4ef draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 04b529c9366e6b77f45bfaa44c1a7fac5772f5b9

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+++ b/test-data/peptide_shaker_certificate_result2.txt	Mon Jun 08 19:54:30 2015 -0400
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+Project Details1: PeptideShaker Version: 0.39.1
+2: Date: Thu Jun 04 20:07:16 CEST 2015
+3: Experiment: Galaxy_Experiment_2015060420071433441234
+4: Sample: Sample_2015060420071433441234
+5: Replicate Number: 1
+6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+ and Comet
+Database Search Parameters
+
+1: Precursor Accuracy Unit: ppm
+2: Precursor Ion m/z Tolerance: 100.0
+3: Fragment Ion m/z Tolerance: 0.5
+4: Enzyme: Trypsin
+5: Number of Missed Cleavages: Not implemented
+6: Database: input_database.fasta
+7: Forward Ion: b
+8: Rewind Ion: y
+9: Fixed Modifications: carbamidomethyl c
+10: Variable Modifications: oxidation of m, acetylation of protein n-term, pyro-cmc, pyro-glu from n-term e, pyro-glu from n-term q
+11: Refinement Variable Modifications: 
+12: Refinement Fixed Modifications: 
+Input Filters
+
+1: Minimal Peptide Length: 1
+2: Maximal Peptide Length: 30
+3: Precursor m/z Tolerance: 10.0
+4: Precursor m/z Tolerance Unit: Yes
+5: Unrecognized Modifications Discarded: No
+Validation Summary
+
+1: #Validated Proteins: 0.0
+2: Protein Total: 0.0
+3Protein FDR Limit: 1.0 %
+4: Protein FNR Limit: 0.0 %
+5: Protein Confidence Limit: -1.0 %
+6: Protein PEP Limit: 101.0 %
+7: Protein Confidence Accuracy: 0.0 %
+8: #Validated Peptides: 0.0
+9: Peptide Total: 0.0
+10: Peptide FDR Limit: 1.0 %
+11: Peptide FNR Limit: 0.0 %
+12: Peptide Confidence Limit: -1.0 %
+13: Peptide PEP Limit: 101.0 %
+14: Peptide Confidence Accuracy: 0.0 %
+15: #Validated PSM: 0.0
+16: PSM Total: 0.0
+17: PSM FDR Limit: 1.0 %
+18: PSM FNR Limit: 0.0 %
+19: PSM Confidence Limit: -1.0 %
+20: PSM PEP Limit: 101.0 %
+21: PSM Confidence Accuracy: 0.0 %
+Postranslational Modification Scoring Settings
+
+1: A-score: No
+2: Accounting for Neutral Losses: No
+3: False Location Rate: 1.0
+Spectrum Counting Parameters
+
+1: Method: NSAF
+2: Validated Matches Only: Yes
+Annotation Settings
+
+1: Intensity Limit: 0.75
+2: Automatic Annotation: Yes
+3: Selected Ions: b, y
+4: Neutral Losses: H2O, NH3
+5: Neutral Losses Sequence Dependence: Yes
+6: Fragment Ion m/z Tolerance: 0.5