# HG changeset patch # User iracooke # Date 1418694811 18000 # Node ID dfb3c79df8e9d584bc882681eb4b61302a3ee8e9 # Parent f1ea11b045d527be73cae1060dbc36a2a2216f94 Deleted selected files diff -r f1ea11b045d5 -r dfb3c79df8e9 macros.xml --- a/macros.xml Mon Dec 15 19:56:40 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,104 +0,0 @@ - - - - - - - - - - -frag_tol "${fragment_tol}" - -prec_tol "${precursor_ion_tol}" - -prec_ppm "${precursor_ion_tol_units}" - -enzyme "${enzyme}" - #set $fixed_mods_str = $fixed_modifications or '' - #set $variable_mods_str = $variable_modifications or '' - #if $fixed_mods_str - -fixed_mods "$fixed_mods_str" - #end if - #if $variable_mods_str - -variable_mods "$variable_mods_str" - #end if - -min_charge $min_charge - -max_charge $max_charge - -mc $missed_cleavages - -fi $forward_ion - -ri $reverse_ion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10.1186/1471-2105-12-70 - 10.1002/pmic.201000595 - - - - diff -r f1ea11b045d5 -r dfb3c79df8e9 peptide_shaker.xml --- a/peptide_shaker.xml Mon Dec 15 19:56:40 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,650 +0,0 @@ - - - Perform protein identification using various search engines based on results from SearchGUI - - - peptide_shaker - - - - -> $temp_stderr) - && - - ###################### - ## PeptideShakerCLI ## - ###################### - (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI - -temp_folder `pwd` - -experiment '${exp_str}' - -sample '${samp_str}' - -replicate 1 - -spectrum_files \$cwd - -identification_files \$cwd/output - -out \$cwd/peptide_shaker_output.cps - -id_params PEPTIDESHAKER_IdentificationParameters.parameters - - -threads "\${GALAXY_SLOTS:-12}" - - ##Optional gene annotation parameter - #if $species_type.species_type_selector != 'no_species_type': - -species_type "${species_type.species_type_selector}" - -species "${species_type.species}" - #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 - #end if - -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" - #end if - - ##Optional filtering parameters: - #if $filtering_options.filtering_options_selector == "yes": - -min_peptide_length "${filtering_options.min_peptide_length}" - -max_peptide_length "${filtering_options.max_peptide_length}" - -max_precursor_error "${filtering_options.max_precursor_error}" - -max_precursor_error_type "${filtering_options.max_precursor_error_type}" - -max_xtandem_e "${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 - - 2>> $temp_stderr) - && - - ################################## - ## PeptideShaker Report options ## - ################################## - (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI - -temp_folder `pwd` - -in \$cwd/peptide_shaker_output.cps - -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 $cleaned_list.remove('mzidentML') - #end if - -reports #echo ','.join($cleaned_list)# - - 2>> $temp_stderr) - && - - #if 'mzidentML' in str($outputs).split(','): - java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI - -in \$cwd/peptide_shaker_output.cps - -output_file output.mzid - -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 - #if '0' in str($outputs).split(','): - find \$cwd/output_reports -name '*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \; - ; - #end if - #if '2' in str($outputs).split(','): - find \$cwd/output_reports -name '*PSM*' -exec bash -c 'mv "$0" "psm.txt"' {} \; - ; - #end if - #if '3' in str($outputs).split(','): - find \$cwd/output_reports -name '*Peptide*' -exec bash -c 'mv "$0" "peptides.txt"' {} \; - ; - #end if - #if '4' in str($outputs).split(','): - find \$cwd/output_reports -name '*Protein*' -exec bash -c 'mv "$0" "proteins.txt"' {} \; - ; - #end if - #if '1' in str($outputs).split(','): - find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \; - ; - #end if - - exit_code_for_galaxy=\$?; - cat $temp_stderr 2>&1; - (exit \$exit_code_for_galaxy) -]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'mzidentML' in outputs - - - 'cps' in outputs - - - '0' in outputs - - - '2' in outputs - - - '3' in outputs - - - '4' in outputs - - - '1' in outputs - - - - - - - - - - - - - - - - - - - - - - - - - - -**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. - -https://code.google.com/p/peptide-shaker/ - -https://code.google.com/p/searchgui/ - ----- - -Reports -======= - - -PSM Report ----------- - -* Protein(s): Protein(s) to which the peptide can be attached -* Sequence: Sequence of the peptide -* Variable Modifications: The variable modifications -* D-score: D-score for variable PTM localization -* probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. -* Localization Confidence: The confidence in variable PTM localization. -* Fixed Modifications: The fixed modifications. -* Spectrum File: The spectrum file. -* Spectrum Title: The title of the spectrum. -* Spectrum Scan Number: The spectrum scan number. -* RT: Retention time -* m/z: Measured m/z -* Measured Charge: The charge as given in the spectrum file. -* Identification Charge: The charge as inferred by the search engine. -* Theoretical Mass: The theoretical mass of the peptide. -* Isotope Number: The isotope number targetted by the instrument. -* Precursor m/z Error: The precursor m/z matching error. -* Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). -* Confidence: Confidence in percent associated to the retained PSM. -* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. - - -Protein Report --------------- - -* Main Accession: Main accession of the protein group. -* Description: Description of the protein designed by the main accession. -* Gene Name: The gene names of the Ensembl gene ID associated to the main accession. -* Chromosome: The chromosome of the Ensembl gene ID associated to the main accession. -* PI: Protein Inference status of the protein group. -* Secondary Accessions: Other accessions in the protein group (alphabetical order). -* Protein Group: The complete protein group (alphabetical order). -* #Peptides: Total number of peptides. -* #Validated Peptides: Number of validated peptides. -* #Unique: Total number of peptides unique to this protein group. -* #PSMs: Number of PSMs -* #Validated PSMs: Number of validated PSMs -* Coverage (%): Sequence coverage in percent of the protein designed by the main accession. -* Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. -* MW (kDa): Molecular Weight. -* Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) -* Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) -* Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized. -* Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized. -* Score: Score of the protein group. -* Confidence: Confidence in percent associated to the protein group. -* Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. - - -Peptide Report --------------- - - -* Protein(s): Protein(s) to which this peptide can be attached. -* AAs Before: The amino-acids before the sequence. -* Sequence: Sequence of the peptide. -* AAs After: The amino-acids after the sequence. -* Modified Sequence: The peptide sequence annotated with variable modifications. -* Variable Modifications: The variable modifications. -* Localization Confidence: The confidence in PTMs localization. -* Fixed Modifications: The fixed modifications. -* #Validated PSMs: Number of validated PSMs. -* #PSMs: Number of PSMs. -* Score: Score of the peptide. -* Confidence: Confidence in percent associated to the peptide. -* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. - - -Hierachical Report ------------------- - -* Main Accession: Main accession of the protein group. -* Description: Description of the protein designed by the main accession. -* PI: Protein Inference status of the protein group. -* Secondary Accessions: Other accessions in the protein group (alphabetical order). -* Protein Group: The complete protein group (alphabetical order). -* #Peptides: Total number of peptides. -* #Validated Peptides: Number of validated peptides. -* #Unique: Total number of peptides unique to this protein group. -* #PSMs: Number of PSMs -* #Validated PSMs: Number of validated PSMs -* Coverage (%): Sequence coverage in percent of the protein designed by the main accession. -* Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. -* MW (kDa): Molecular Weight. -* Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) -* Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) -* Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized. -* Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized. -* Score: Score of the protein group. -* Confidence: Confidence in percent associated to the protein group. -* Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. -* Protein(s): Protein(s) to which this peptide can be attached. -* AAs Before: The amino-acids before the sequence. -* Sequence: Sequence of the peptide. -* AAs After: The amino-acids after the sequence. -* Variable Modifications: The variable modifications. -* Localization Confidence: The confidence in PTMs localization. -* Fixed Modifications: The fixed modifications. -* #Validated PSMs: Number of validated PSMs. -* #PSMs: Number of PSMs. -* Score: Score of the peptide. -* Confidence: Confidence in percent associated to the peptide. -* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. -* Protein(s): Protein(s) to which the peptide can be attached. -* Sequence: Sequence of the peptide. -* Modified Sequence: The peptide sequence annotated with variable modifications. -* Variable Modifications: The variable modifications. -* D-score: D-score for variable PTM localization. -* probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. -* Localization Confidence: The confidence in variable PTM localization. -* Fixed Modifications: The fixed modifications. -* Spectrum File: The spectrum file. -* Spectrum Title: The title of the spectrum. -* Spectrum Scan Number: The spectrum scan number. -* RT: Retention time -* m/z: Measured m/z -* Measured Charge: The charge as given in the spectrum file. -* Identification Charge: The charge as inferred by the search engine. -* Theoretical Mass: The theoretical mass of the peptide. -* Isotope Number: The isotope number targetted by the instrument. -* Precursor m/z Error: The precursor m/z matching error. -* Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). -* Confidence: Confidence in percent associated to the retained PSM. -* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. - - - - ------- - -**Citation** - -To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com - -If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker - - - diff -r f1ea11b045d5 -r dfb3c79df8e9 repository_dependencies.xml --- a/repository_dependencies.xml Mon Dec 15 19:56:40 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - diff -r f1ea11b045d5 -r dfb3c79df8e9 searchgui.xml --- a/searchgui.xml Mon Dec 15 19:56:40 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,343 +0,0 @@ - - - Perform protein identification using various search engines and prepare results for input to Peptide Shaker - - - searchgui - - - - - $temp_stderr) - && - - ################ - ## Search CLI ## - ################ - (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI - -temp_folder `pwd` - -spectrum_files \$cwd - -output_folder \$cwd/output - -id_params SEARCHGUI_IdentificationParameters.parameters - - -threads "\${GALAXY_SLOTS:-12}" - -correct_titles "${correct_titles}" - $missing_titles - -mgf_splitting "${mgf_splitting}" - -mgf_spectrum_count "${mgf_spectrum_count}" - - ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created - ## the tree is generated afterwards in PeptideShaker - -protein_index 0 - - ##-makeblastdb_folder \$BLAST_ROOT_DIR - - #if $advanced.advanced_type_selector == "advanced": - - #if $advanced.xtandem.xtandem_selector == "yes" - -xtandem 1 - #else - -xtandem 0 - #end if - - #if $advanced.omssa.omssa_selector == "yes" - -omssa 1 - #else - -omssa 0 - #end if - - #if $advanced.msgf.msgf_selector == "yes" - -msgf 1 - #else - -msgf 0 - #end if - - #if $advanced.ms_amanda.ms_amanda_selector == "yes" - -ms_amanda 1 - #else - -ms_amanda 0 - #end if - - #if $advanced.myrimatch.myrimatch_selector == "yes" - -myrimatch 1 - #else - -myrimatch 0 - #end if - - #if $advanced.comet.comet_selector == "yes" - -comet 1 - #else - -comet 0 - #end if - - #else - -ms_amanda 0 - #end if - - ## single zip file - -output_option 0 - - 2>> $temp_stderr) - - && - - exit_code_for_galaxy=\$?; - cat $temp_stderr 2>&1; - (exit \$exit_code_for_galaxy) -]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**What it does** - -Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI. - - - - - diff -r f1ea11b045d5 -r dfb3c79df8e9 searchgui_mods.loc.sample --- a/searchgui_mods.loc.sample Mon Dec 15 19:56:40 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,210 +0,0 @@ -methylation of k -oxidation of m -carboxymethyl c -carbamidomethyl c -deamidation of n and q -propionamide c -phosphorylation of s -phosphorylation of t -phosphorylation of y -m cleavage from protein n-term -acetylation of protein n-term -methylation of protein n-term -tri-methylation of protein n-term -beta methythiolation of d -methylation of q -tri-methylation of k -methylation of d -methylation of e -methylation of peptide c-term -tri-deuteromethylation of d -tri-deuteromethylation of e -tri-deuteromethylation of peptide c-term -n-formyl met addition -2-amino-3-oxo-butanoic acid t -acetylation of k -amidation of peptide c-term -beta-methylthiolation of d (duplicate of 13) -carboxyamidomethylation of k -carboxyamidomethylation of h -carboxyamidomethylation of d -carboxyamidomethylation of e -carbamylation of k -carbamylation of n-term peptide -citrullination of r -oxidation of c to cysteic acid -di-iodination of y -di-methylation of k -di-methylation of r -di-methylation of peptide n-term -oxidation of f to dihydroxyphenylalanine -gammathiopropionylation of k -gammathiopropionylation of peptide n-term -farnesylation of c -formylation of k -formylation of peptide n-term -oxidation of w to formylkynurenin -fluorophenylalanine -beta-carboxylation of d -gamma-carboxylation of e -geranyl-geranyl -glucuronylation of protein n-term -glutathione disulfide -ubiquitinylation residue -guanidination of k -oxidation of h to n -oxidation of h to d -homoserine -homoserine lactone -oxidation of w to hydroxykynurenin -hydroxylation of d -hydroxylation of k -hydroxylation of n -hydroxylation of p -hydroxylation of f -hydroxylation of y -iodination of y -oxidation of w to kynurenin -lipoyl k -methyl ester of peptide c-term (duplicate of 18) -methyl ester of d -methyl ester of e (duplicate of 17) -methyl ester of s -methyl ester of y -methyl c -methyl h -methyl n -methylation of peptide n-term -methyl r -myristoleylation of g -myristoyl-4h of g -myristoylation of peptide n-term g -myristoylation of k -formylation of protein n-term -nem c -nipcam -oxidation of w to nitro -oxidation of y to nitro -o18 on peptide n-term -di-o18 on peptide n-term -oxidation of h -oxidation of w -phosphopantetheine s -palmitoylation of c -palmitoylation of k -palmitoylation of s -palmitoylation of t -phosphorylation of s with prompt loss -phosphorylation of t with prompt loss -phosphorylation with prompt loss on y -phosphorylation with neutral loss on c -phosphorylation with neutral loss on d -phosphorylation with neutral loss on h -propionyl light k -propionyl light on peptide n-term -propionyl heavy k -propionyl heavy peptide n-term -pyridyl k -pyridyl peptide n-term -pyro-cmc -pyro-glu from n-term e -pyro-glu from n-term q -oxidation of p to pyroglutamic acid -s-pyridylethylation of c -semet -sulfation of y -sulphone of m -tri-iodination of y -tri-methylation of r -n-acyl diglyceride cysteine -icat light -icat heavy -camthiopropanoyl k -phosphorylation with neutral loss on s -phosphorylation with neutral loss on t -phosphorylation of s with etd loss -phosphorylation of t with etd loss -heavy arginine-13c6 -heavy arginine-13c6-15n4 -heavy lysine-13c6 -pngasf in o18 water -beta elimination of s -beta elimination of t -oxidation of c to sulfinic acid -arginine to ornithine -dehydro of s and t -carboxykynurenin of w -sumoylation of k -itraq114 on nterm -itraq114 on k -itraq114 on y -itraq115 on nterm -itraq115 on k -itraq115 on y -itraq116 on nterm -itraq116 on k -itraq116 on y -itraq117 on nterm -itraq117 on k -itraq117 on y -mmts on c -heavy lysine - 2h4 -heavy lysine - 13c6 15n2 -asparagine hexnac -asparagine dhexhexnac -serine hexnac -threonine hexnac -palmitoleyl of s -palmitoleyl of c -palmitoleyl of t -chd2-di-methylation of k -chd2-di-methylation of peptide n-term -maleimide-peo2-biotin of c -phosphorylation of h -oxidation of c -oxidation of y (duplicate of 64) -uniblue a on k -deamidation of n -trideuteration of l (silac) -tmt duplex on k -tmt duplex on n-term peptide -tmt 6-plex on k -tmt 6-plex on n-term peptide -itraq8plex:13c(7)15n(1) on nterm -itraq8plex:13c(7)15n(1) on k -itraq8plex:13c(7)15n(1) on y -itraq8plex:13c(6)15n(2) on nterm -itraq8plex:13c(6)15n(2) on k -itraq8plex:13c(6)15n(2) on y -selenocysteine -carboxymethylated selenocysteine -dimethyl 2d n-terminus -dimethyl 2d k -gtp desthiobiotinc12 -gtp desthiobiotinc13 -user modification 5 -user modification 6 -user modification 7 -user modification 8 -user modification 9 -user modification 10 -user modification 11 -user modification 12 -user modification 13 -user modification 14 -user modification 15 -user modification 16 -user modification 17 -user modification 18 -user modification 19 -user modification 20 -user modification 21 -user modification 22 -user modification 23 -user modification 24 -user modification 25 -user modification 26 -user modification 27 -user modification 28 -user modification 29 -user modification 30 diff -r f1ea11b045d5 -r dfb3c79df8e9 tool_dependencies.xml --- a/tool_dependencies.xml Mon Dec 15 19:56:40 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ - - - - - - - - -