# HG changeset patch # User iracooke # Date 1402698391 14400 # Node ID 75184e45bf84a68da70712c9cfe90b97e7665da0 # Parent f36b84d1ac09bd1c8bee293b228b77063ee94cbf Uploaded diff -r f36b84d1ac09 -r 75184e45bf84 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Fri Jun 13 18:26:31 2014 -0400 @@ -0,0 +1,9 @@ +This includes tools for running Mascot MS/MS searches + +Running this tool requires a working installation of Mascot (commercial software). +Mascot is available from http://www.matrixscience.com/ + +Requirements: +This package uses protk which must be installed separately. + +For instructions please see: https://github.com/iracooke/protk/#galaxy-integration diff -r f36b84d1ac09 -r 75184e45bf84 mascot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mascot.xml Fri Jun 13 18:26:31 2014 -0400 @@ -0,0 +1,205 @@ + + + + protk + + + Mascot MS/MS Search + + + mascot_search.rb + + #if $database.source_select=="built_in": + -d $database.dbkey + #else + -d $database.custom_db + #end if + + -f $fragment_ion_tol + + -S $server $input_file + + -o $output + + -r + + ## Variable Mods + + --var-mods=' + $variable_mods + ' + + --fix-mods=' + $fixed_mods + ' + --allowed-charges=$allowed_charges + + --enzyme=$enzyme + + --instrument=$instrument + + --precursor-ion-tol-units=$precursor_tolu + + --email=$email + + -v $missed_cleavages + + #if $security.security_use + --use-security + --username $security.username + --password $security.password + #end if + + #if $proxy + --proxy $proxy + #end if + + + + + + + + + + + + + + + Database + + + + + + + + + + + + + + + + + + + + + + + + + + + Missed Cleavages Allowed + + + + + + + Enzyme + + + + + + + + + + + + + + + + + + + + + + + + + Peptide Charge + + + + + + + + + + + + + + + + + + + + + + + + + + + Instrument + + + + + + + + + + + + + + + + + + + + Precursor Ion Tolerance Units + + + + + + + + + + + + + + + + + + + + + + + + + + Run a Mascot MS/MS Ion Search + + + diff -r f36b84d1ac09 -r 75184e45bf84 mascot_to_pepxml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mascot_to_pepxml.xml Fri Jun 13 18:26:31 2014 -0400 @@ -0,0 +1,82 @@ + + + protk + trans_proteomic_pipeline + + + Converts a mascot results file to pepXML + +mascot_to_pepxml.rb + $input_file + + -o $output + + #if $database.source_select=="built_in": + -d $database.dbkey + #else + -d $database.fasta_file + #end if + + #if $explicit_enzyme.explicit_enzyme_use + --enzyme $explicit_enzyme.enzyme + #end if + + $shortid + + + + + + + + + + + + + + + Database + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Convert mascot results from mascotdat to pepXML + + + diff -r f36b84d1ac09 -r 75184e45bf84 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Jun 13 18:26:31 2014 -0400 @@ -0,0 +1,4 @@ + + + + diff -r f36b84d1ac09 -r 75184e45bf84 tool-data/mascot_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mascot_databases.loc.sample Fri Jun 13 18:26:31 2014 -0400 @@ -0,0 +1,13 @@ +#This file lists the names of protein databases installed on Mascot +# +#In order to use interprophet to combine results from different search engines +#it is important that all searches are performed on the same database +#you should therefore ensure that each database installed on mascot has an equivalent +#database installed in the Protk databases directory (databases used by omssa and x!tandem) +#the mascot_to_pepxml tool will ask for this database when performing the conversion. +# +# Entries should follow the be structured as follows +# Display_name dbkey dbNameOnMascot dbkey +# +Swissprot spall_ SwissProt spall_ +Swissprot Human sphuman_ SPHuman sphuman_ \ No newline at end of file diff -r f36b84d1ac09 -r 75184e45bf84 tool-data/mascot_mods.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mascot_mods.loc.sample Fri Jun 13 18:26:31 2014 -0400 @@ -0,0 +1,77 @@ +#This file lists the names of chemical modifications acceptable for proteomics search engines +# +# +Acetyl (K) acetyl_k_ Acetyl (K) acetyl_k_ +Acetyl (N-term) acetyl_n-term_ Acetyl (N-term) acetyl_n-term_ +Acetyl (Protein N-term) acetyl_proteinn-term_ Acetyl (Protein N-term) acetyl_proteinn-term_ +Amidated (C-term) amidated_c-term_ Amidated (C-term) amidated_c-term_ +Amidated (Protein C-term) amidated_proteinc-term_ Amidated (Protein C-term) amidated_proteinc-term_ +Ammonia-loss (N-term C) ammonia-loss_n-termc_ Ammonia-loss (N-term C) ammonia-loss_n-termc_ +Biotin (K) biotin_k_ Biotin (K) biotin_k_ +Biotin (N-term) biotin_n-term_ Biotin (N-term) biotin_n-term_ +Carbamidomethyl (C) carbamidomethyl_c_ Carbamidomethyl (C) carbamidomethyl_c_ +Carbamyl (K) carbamyl_k_ Carbamyl (K) carbamyl_k_ +Carbamyl (N-term) carbamyl_n-term_ Carbamyl (N-term) carbamyl_n-term_ +Carboxymethyl (C) carboxymethyl_c_ Carboxymethyl (C) carboxymethyl_c_ +Cation:Na (C-term) cation_na_c-term_ Cation:Na (C-term) cation_na_c-term_ +Cation:Na (DE) cation_na_de_ Cation:Na (DE) cation_na_de_ +Deamidated (NQ) deamidated_nq_ Deamidated (NQ) deamidated_nq_ +Deamidated-N (N) deamidated-n_n_ Deamidated-N (N) deamidated-n_n_ +Dehydrated (N-term C) dehydrated_n-termc_ Dehydrated (N-term C) dehydrated_n-termc_ +Dehydro (C) dehydro_c_ Dehydro (C) dehydro_c_ +Dioxidation (M) dioxidation_m_ Dioxidation (M) dioxidation_m_ +Ethanolyl (C) ethanolyl_c_ Ethanolyl (C) ethanolyl_c_ +ExacTagAmine (K) exactagamine_k_ ExacTagAmine (K) exactagamine_k_ +ExacTagThiol (C) exactagthiol_c_ ExacTagThiol (C) exactagthiol_c_ +Formyl (N-term) formyl_n-term_ Formyl (N-term) formyl_n-term_ +Formyl (Protein N-term) formyl_proteinn-term_ Formyl (Protein N-term) formyl_proteinn-term_ +Gln->pyro-Glu (N-term Q) gln_pyro-glu_n-termq_ Gln->pyro-Glu (N-term Q) gln_pyro-glu_n-termq_ +Glu->pyro-Glu (N-term E) glu_pyro-glu_n-terme_ Glu->pyro-Glu (N-term E) glu_pyro-glu_n-terme_ +Guanidinyl (K) guanidinyl_k_ Guanidinyl (K) guanidinyl_k_ +ICAT-C (C) icat-c_c_ ICAT-C (C) icat-c_c_ +ICAT-C:13C(9) (C) icat-c_13c_9__c_ ICAT-C:13C(9) (C) icat-c_13c_9__c_ +ICPL (K) icpl_k_ ICPL (K) icpl_k_ +ICPL (Protein N-term) icpl_proteinn-term_ ICPL (Protein N-term) icpl_proteinn-term_ +ICPL:13C(6) (K) icpl_13c_6__k_ ICPL:13C(6) (K) icpl_13c_6__k_ +ICPL:13C(6) (Protein N-term) icpl_13c_6__proteinn-term_ ICPL:13C(6) (Protein N-term) icpl_13c_6__proteinn-term_ +ICPL:13C(6)2H(4) (K) icpl_13c_6_2h_4__k_ ICPL:13C(6)2H(4) (K) icpl_13c_6_2h_4__k_ +ICPL:13C(6)2H(4) (N-term) icpl_13c_6_2h_4__n-term_ ICPL:13C(6)2H(4) (N-term) icpl_13c_6_2h_4__n-term_ +ICPL:13C(6)2H(4) (Protein N-term) icpl_13c_6_2h_4__proteinn-term_ ICPL:13C(6)2H(4) (Protein N-term) icpl_13c_6_2h_4__proteinn-term_ +ICPL:2H(4) (K) icpl_2h_4__k_ ICPL:2H(4) (K) icpl_2h_4__k_ +ICPL:2H(4) (Protein N-term) icpl_2h_4__proteinn-term_ ICPL:2H(4) (Protein N-term) icpl_2h_4__proteinn-term_ +iTRAQ4plex (K) itraq4plex_k_ iTRAQ4plex (K) itraq4plex_k_ +iTRAQ4plex (N-term) itraq4plex_n-term_ iTRAQ4plex (N-term) itraq4plex_n-term_ +iTRAQ4plex (Y) itraq4plex_y_ iTRAQ4plex (Y) itraq4plex_y_ +iTRAQ8plex (K) itraq8plex_k_ iTRAQ8plex (K) itraq8plex_k_ +iTRAQ8plex (N-term) itraq8plex_n-term_ iTRAQ8plex (N-term) itraq8plex_n-term_ +iTRAQ8plex (Y) itraq8plex_y_ iTRAQ8plex (Y) itraq8plex_y_ +Label:18O(1) (C-term) label_18o_1__c-term_ Label:18O(1) (C-term) label_18o_1__c-term_ +Label:18O(2) (C-term) label_18o_2__c-term_ Label:18O(2) (C-term) label_18o_2__c-term_ +Met->Hse (C-term M) met_hse_c-termm_ Met->Hse (C-term M) met_hse_c-termm_ +Met->Hsl (C-term M) met_hsl_c-termm_ Met->Hsl (C-term M) met_hsl_c-termm_ +Methyl (C-term) methyl_c-term_ Methyl (C-term) methyl_c-term_ +Methyl (DE) methyl_de_ Methyl (DE) methyl_de_ +Methylthio (C) methylthio_c_ Methylthio (C) methylthio_c_ +mTRAQ (K) mtraq_k_ mTRAQ (K) mtraq_k_ +mTRAQ (N-term) mtraq_n-term_ mTRAQ (N-term) mtraq_n-term_ +mTRAQ (Y) mtraq_y_ mTRAQ (Y) mtraq_y_ +mTRAQ:13C(3)15N(1) (K) mtraq_13c_3_15n_1__k_ mTRAQ:13C(3)15N(1) (K) mtraq_13c_3_15n_1__k_ +mTRAQ:13C(3)15N(1) (N-term) mtraq_13c_3_15n_1__n-term_ mTRAQ:13C(3)15N(1) (N-term) mtraq_13c_3_15n_1__n-term_ +mTRAQ:13C(3)15N(1) (Y) mtraq_13c_3_15n_1__y_ mTRAQ:13C(3)15N(1) (Y) mtraq_13c_3_15n_1__y_ +NIPCAM (C) nipcam_c_ NIPCAM (C) nipcam_c_ +Oxidation (HW) oxidation_hw_ Oxidation (HW) oxidation_hw_ +Oxidation (M) oxidation_m_ Oxidation (M) oxidation_m_ +Phospho (ST) phospho_st_ Phospho (ST) phospho_st_ +Phospho (Y) phospho_y_ Phospho (Y) phospho_y_ +Propionamide (C) propionamide_c_ Propionamide (C) propionamide_c_ +Pyridylethyl (C) pyridylethyl_c_ Pyridylethyl (C) pyridylethyl_c_ +Pyro-carbamidomethyl (N-term C) pyro-carbamidomethyl_n-termc_ Pyro-carbamidomethyl (N-term C) pyro-carbamidomethyl_n-termc_ +Sulfo (S) sulfo_s_ Sulfo (S) sulfo_s_ +Sulfo (T) sulfo_t_ Sulfo (T) sulfo_t_ +Sulfo (Y) sulfo_y_ Sulfo (Y) sulfo_y_ +TMT (K) tmt_k_ TMT (K) tmt_k_ +TMT (N-term) tmt_n-term_ TMT (N-term) tmt_n-term_ +TMT2plex (K) tmt2plex_k_ TMT2plex (K) tmt2plex_k_ +TMT2plex (N-term) tmt2plex_n-term_ TMT2plex (N-term) tmt2plex_n-term_ +TMT6plex (K) tmt6plex_k_ TMT6plex (K) tmt6plex_k_ +TMT6plex (N-term) tmt6plex_n-term_ TMT6plex (N-term) tmt6plex_n-term_ diff -r f36b84d1ac09 -r 75184e45bf84 tool-data/pepxml_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pepxml_databases.loc.sample Fri Jun 13 18:26:31 2014 -0400 @@ -0,0 +1,13 @@ +#This file lists the names of protein databases installed locally in protk. +# These are used by omssa and x!tandem as well as the "mascot to pepxml" tool +# In order to combine search results with Interprophet searches must be run against an identical database +# +# Entries should follow the be structured as follows +# Display_name omssa_tandem_dbname dbkey +# +# +Swissprot spall_ SwissProt spall_ +Combined PlasmboDB (falciparum) and Swissprot Human plasmodb_pfalciparum_sphuman_ plasmodb_pfalciparum_sphuman plasmodb_pfalciparum_sphuman_ +Swissprot Human sphuman_ sphuman sphuman_ +Combined Swissprot/TRembl Human sptrhuman_ sptrhuman sptrhuman_ +Swissprot Mouse spmouse_ spmouse spmouse_