| Previous changeset 57:da885ca16cb2 (2021-03-16) Next changeset 59:943a34df6047 (2021-05-21) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" |
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modified:
fasta_cli.xml ident_params.xml macros_basic.xml peptide_shaker.xml searchgui.xml test-data/peptideshaker_reports_output_certificate.txt test-data/peptideshaker_reports_output_extendedpsm.tabular test-data/peptideshaker_reports_output_hierarchical.tabular test-data/peptideshaker_reports_output_peptides.tabular test-data/peptideshaker_reports_output_peptidesnonvalidated.tabular test-data/peptideshaker_reports_output_peptidesphosphorylation.tabular test-data/peptideshaker_reports_output_proteins.tabular test-data/peptideshaker_reports_output_proteinsnonvalidated.tabular test-data/peptideshaker_reports_output_proteinsphosphorylation.tabular test-data/peptideshaker_reports_output_psm.tabular test-data/peptideshaker_reports_output_psmnonvalidated.tabular test-data/peptideshaker_reports_output_psmphosphorylation.tabular |
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| diff -r da885ca16cb2 -r 07ff622ec007 fasta_cli.xml --- a/fasta_cli.xml Tue Mar 16 15:12:03 2021 +0000 +++ b/fasta_cli.xml Sat Apr 10 15:57:17 2021 +0000 |
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| @@ -1,6 +1,6 @@ <tool id="fasta_cli" name="FastaCLI" - version="1.0.1" + version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@" profile="20.01" > <description> |
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| diff -r da885ca16cb2 -r 07ff622ec007 ident_params.xml --- a/ident_params.xml Tue Mar 16 15:12:03 2021 +0000 +++ b/ident_params.xml Sat Apr 10 15:57:17 2021 +0000 |
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| @@ -1,6 +1,6 @@ <tool id="ident_params" name="Identification Parameters" - version="1.5.1" + version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@" profile="20.01" > <description> |
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| diff -r da885ca16cb2 -r 07ff622ec007 macros_basic.xml --- a/macros_basic.xml Tue Mar 16 15:12:03 2021 +0000 +++ b/macros_basic.xml Sat Apr 10 15:57:17 2021 +0000 |
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| @@ -11,9 +11,9 @@ </stdio> </xml> <token name="@SEARCHGUI_MAJOR_VERSION@">4</token> - <token name="@SEARCHGUI_VERSION@">4.0.22</token> + <token name="@SEARCHGUI_VERSION@">4.0.25</token> <token name="@SEARCHGUI_VERSION_SUFFIX@">0</token> - <token name="@PEPTIDESHAKER_VERSION@">2.0.15</token> + <token name="@PEPTIDESHAKER_VERSION@">2.0.18</token> <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">0</token> <xml name="citations"> <citations> |
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| diff -r da885ca16cb2 -r 07ff622ec007 peptide_shaker.xml --- a/peptide_shaker.xml Tue Mar 16 15:12:03 2021 +0000 +++ b/peptide_shaker.xml Sat Apr 10 15:57:17 2021 +0000 |
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| @@ -570,10 +570,15 @@ <tests> <!-- Basic test: default identification parameters, searchgui_tinydb1.fasta, 4 search engines xx--> - <test expect_num_outputs="1"> + <test expect_num_outputs="2"> <param name="searchgui_input" value="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive"/> - <param name="mzidentml_creation" value="0"/> + <param name="mzidentml_creation" value="1"/> <param name="export_psdb" value="1"/> + <output name="mzidentML" ftype="mzid"> + <assert_contents> + <has_text text="MzIdentML"/> + </assert_contents> + </output> <output name="output_psdb" ftype="peptideshaker_archive"> <assert_contents> <has_size value="122880" delta="3000"/> |
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| diff -r da885ca16cb2 -r 07ff622ec007 searchgui.xml --- a/searchgui.xml Tue Mar 16 15:12:03 2021 +0000 +++ b/searchgui.xml Sat Apr 10 15:57:17 2021 +0000 |
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| @@ -170,7 +170,7 @@ <inputs> <param format="json" name="input_parameters_file" type="data" label="Identification Parameters file"/> - <param format="fasta" name="input_fasta_file" type="data" label="Fasta file"/> + <param format="fasta" name="input_fasta_file" type="data" label="Fasta file" help="For postprocessing with PeptideShaker the sequences must have UniProt style headers and contain decoy sequences (see help)."/> <param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists" help="Select appropriate MGF/MZML dataset(s) from history" /> @@ -326,6 +326,21 @@ Optional: MyriMatch, MS-Amanda, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed. +**Input FASTA** + +In order to allow for postprocessing with PeptideShaker the sequences must contain decoy sequences (see _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#decoy-sequences) +and the FASTA header must either contain no "|" characters (then the whole header will be used as ID) or have the following format: + + >generic[your tag]|[protein accession]|[protein description] + + or + + >generic[your tag]|[protein accession] + +See _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#non-standard-fasta. + + + </help> <expand macro="citations" /> </tool> |
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| diff -r da885ca16cb2 -r 07ff622ec007 test-data/peptideshaker_reports_output_certificate.txt --- a/test-data/peptideshaker_reports_output_certificate.txt Tue Mar 16 15:12:03 2021 +0000 +++ b/test-data/peptideshaker_reports_output_certificate.txt Sat Apr 10 15:57:17 2021 +0000 |
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| @@ -1,9 +1,9 @@ Project Details -1: PeptideShaker Version: 2.0.2 -2: Date: Thu Nov 19 10:47:40 CET 2020 -3: Experiment: Galaxy_Experiment_2020111910471605779259 +1: PeptideShaker Version: 2.0.18 +2: Date: Fri Apr 02 17:00:43 GMT 2021 +3: Experiment: Galaxy_Experiment_2021040219001617382836 4: Sample: Not implemented 5: Replicate Number: Not implemented 6: Identification Algorithms: OMSSA, X!Tandem and MS-GF+ |
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| diff -r da885ca16cb2 -r 07ff622ec007 test-data/peptideshaker_reports_output_proteins.tabular --- a/test-data/peptideshaker_reports_output_proteins.tabular Tue Mar 16 15:12:03 2021 +0000 +++ b/test-data/peptideshaker_reports_output_proteins.tabular Sat Apr 10 15:57:17 2021 +0000 |
| [ |
| @@ -1,5 +1,5 @@ - Protein Inference Main Accession Description Protein Group Secondary Accessions Chromosome Gene Name Taxonomy Validated Coverage [%] All Coverage [%] Possible Coverage [%] #Peptides #Validated Peptides #Unique Peptides #Validated Unique Peptides #PSMs #Validated PSMs Confidently Localized Modification Sites #Confidently Localized Modification Sites Ambiguously Localized Modification Sites #Ambiguously Localized Modification Sites Spectrum Counting MW [kDa] Confidence [%] Validation -1 Single Protein cds.comp8310_c0_seq2 m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 cds.comp8310_c0_seq2 3.69 3.69 81.0 1 1 1 1 1 1 12239.035185720222 45.26545451338222 100.0 Doubtful -2 Single Protein cds.comp41890_c0_seq1 m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 cds.comp41890_c0_seq1 20.15 20.15 91.04 1 1 1 1 1 1 30798.227885377935 14.802380493830709 100.0 Doubtful -3 Related Proteins cds.comp41779_c0_seq1 m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 3.34 3.34 78.82 1 1 1 1 1 1 7590.674347507289 69.88215380565931 100.0 Doubtful -4 Single Protein cds.comp41890_c0_seq1_REVERSED m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED cds.comp41890_c0_seq1_REVERSED 8.21 8.21 90.3 1 1 1 1 1 1 31052.758694348 14.802380493830709 100.0 Doubtful + Protein Inference Main Accession Description Protein Group Secondary Accessions Chromosome Gene Name Taxonomy Organism Identifier Validated Coverage [%] All Coverage [%] Possible Coverage [%] #Peptides #Validated Peptides #Unique Peptides #Validated Unique Peptides #PSMs #Validated PSMs Confidently Localized Modification Sites #Confidently Localized Modification Sites Ambiguously Localized Modification Sites #Ambiguously Localized Modification Sites Spectrum Counting MW [kDa] Confidence [%] Validation +1 Single Protein cds.comp8310_c0_seq2 m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 cds.comp8310_c0_seq2 3.69 3.69 81.0 1 1 1 1 1 1 12239.035185720222 45.26545451338222 100.0 Doubtful +2 Single Protein cds.comp41890_c0_seq1 m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 cds.comp41890_c0_seq1 20.15 20.15 91.04 1 1 1 1 1 1 30798.227885377935 14.802380493830709 100.0 Doubtful +3 Related Proteins cds.comp41779_c0_seq1 m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 3.34 3.34 78.82 1 1 1 1 1 1 7590.674347507289 69.88215380565931 100.0 Doubtful +4 Single Protein cds.comp41890_c0_seq1_REVERSED m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED cds.comp41890_c0_seq1_REVERSED 8.21 8.21 90.3 1 1 1 1 1 1 31052.758694348 14.802380493830709 100.0 Doubtful |
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| diff -r da885ca16cb2 -r 07ff622ec007 test-data/peptideshaker_reports_output_proteinsnonvalidated.tabular --- a/test-data/peptideshaker_reports_output_proteinsnonvalidated.tabular Tue Mar 16 15:12:03 2021 +0000 +++ b/test-data/peptideshaker_reports_output_proteinsnonvalidated.tabular Sat Apr 10 15:57:17 2021 +0000 |
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| @@ -1,5 +1,5 @@ - Protein Inference Main Accession Description Protein Group Secondary Accessions Chromosome Gene Name Taxonomy Validated Coverage [%] All Coverage [%] Possible Coverage [%] #Peptides #Validated Peptides #Unique Peptides #Validated Unique Peptides #PSMs #Validated PSMs Confidently Localized Modification Sites #Confidently Localized Modification Sites Ambiguously Localized Modification Sites #Ambiguously Localized Modification Sites Spectrum Counting MW [kDa] Confidence [%] Validation -1 Single Protein cds.comp8310_c0_seq2 m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 cds.comp8310_c0_seq2 3.69 3.69 81.0 1 1 1 1 1 1 12239.035185720222 45.26545451338222 100.0 Doubtful -2 Single Protein cds.comp41890_c0_seq1 m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 cds.comp41890_c0_seq1 20.15 20.15 91.04 1 1 1 1 1 1 30798.227885377935 14.802380493830709 100.0 Doubtful -3 Related Proteins cds.comp41779_c0_seq1 m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 3.34 3.34 78.82 1 1 1 1 1 1 7590.674347507289 69.88215380565931 100.0 Doubtful -4 Single Protein cds.comp41890_c0_seq1_REVERSED m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED cds.comp41890_c0_seq1_REVERSED 8.21 8.21 90.3 1 1 1 1 1 1 31052.758694348 14.802380493830709 100.0 Doubtful + Protein Inference Main Accession Description Protein Group Secondary Accessions Chromosome Gene Name Taxonomy Organism Identifier Validated Coverage [%] All Coverage [%] Possible Coverage [%] #Peptides #Validated Peptides #Unique Peptides #Validated Unique Peptides #PSMs #Validated PSMs Confidently Localized Modification Sites #Confidently Localized Modification Sites Ambiguously Localized Modification Sites #Ambiguously Localized Modification Sites Spectrum Counting MW [kDa] Confidence [%] Validation +1 Single Protein cds.comp8310_c0_seq2 m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 cds.comp8310_c0_seq2 3.69 3.69 81.0 1 1 1 1 1 1 12239.035185720222 45.26545451338222 100.0 Doubtful +2 Single Protein cds.comp41890_c0_seq1 m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 cds.comp41890_c0_seq1 20.15 20.15 91.04 1 1 1 1 1 1 30798.227885377935 14.802380493830709 100.0 Doubtful +3 Related Proteins cds.comp41779_c0_seq1 m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 3.34 3.34 78.82 1 1 1 1 1 1 7590.674347507289 69.88215380565931 100.0 Doubtful +4 Single Protein cds.comp41890_c0_seq1_REVERSED m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED cds.comp41890_c0_seq1_REVERSED 8.21 8.21 90.3 1 1 1 1 1 1 31052.758694348 14.802380493830709 100.0 Doubtful |
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| diff -r da885ca16cb2 -r 07ff622ec007 test-data/peptideshaker_reports_output_proteinsphosphorylation.tabular --- a/test-data/peptideshaker_reports_output_proteinsphosphorylation.tabular Tue Mar 16 15:12:03 2021 +0000 +++ b/test-data/peptideshaker_reports_output_proteinsphosphorylation.tabular Sat Apr 10 15:57:17 2021 +0000 |
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| @@ -1,5 +1,5 @@ - Protein Inference Main Accession Description Protein Group Secondary Accessions Chromosome Gene Name Taxonomy Validated Coverage [%] All Coverage [%] Possible Coverage [%] #Peptides #Validated Peptides #Unique Peptides #Validated Unique Peptides #PSMs #Validated PSMs Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites Spectrum Counting NSAF MW [kDa] Confidence [%] Validation -1 Single Protein cds.comp8310_c0_seq2 m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 cds.comp8310_c0_seq2 3.69 3.69 81.0 1 1 1 1 1 1 0 0 0.003257328990228013 45.26545451338222 100.0 Doubtful -2 Single Protein cds.comp41890_c0_seq1 m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 cds.comp41890_c0_seq1 20.15 20.15 91.04 1 1 1 1 1 1 0 0 0.00819672131147541 14.802380493830709 100.0 Doubtful -3 Related Proteins cds.comp41779_c0_seq1 m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 3.34 3.34 78.82 1 1 1 1 1 1 0 0 0.00202020202020202 69.88215380565931 100.0 Doubtful -4 Single Protein cds.comp41890_c0_seq1_REVERSED m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED cds.comp41890_c0_seq1_REVERSED 8.21 8.21 90.3 1 1 1 1 1 1 0 0 0.008264462809917356 14.802380493830709 100.0 Doubtful + Protein Inference Main Accession Description Protein Group Secondary Accessions Chromosome Gene Name Taxonomy Organism Identifier Validated Coverage [%] All Coverage [%] Possible Coverage [%] #Peptides #Validated Peptides #Unique Peptides #Validated Unique Peptides #PSMs #Validated PSMs Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites Spectrum Counting NSAF MW [kDa] Confidence [%] Validation +1 Single Protein cds.comp8310_c0_seq2 m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 cds.comp8310_c0_seq2 3.69 3.69 81.0 1 1 1 1 1 1 0 0 0.003257328990228013 45.26545451338222 100.0 Doubtful +2 Single Protein cds.comp41890_c0_seq1 m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 cds.comp41890_c0_seq1 20.15 20.15 91.04 1 1 1 1 1 1 0 0 0.00819672131147541 14.802380493830709 100.0 Doubtful +3 Related Proteins cds.comp41779_c0_seq1 m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 3.34 3.34 78.82 1 1 1 1 1 1 0 0 0.00202020202020202 69.88215380565931 100.0 Doubtful +4 Single Protein cds.comp41890_c0_seq1_REVERSED m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED cds.comp41890_c0_seq1_REVERSED 8.21 8.21 90.3 1 1 1 1 1 1 0 0 0.008264462809917356 14.802380493830709 100.0 Doubtful |