# HG changeset patch # User iracooke # Date 1402698375 14400 # Node ID f36b84d1ac09bd1c8bee293b228b77063ee94cbf # Parent 327b2d99d4c5f7586a1427a7812bfbd906ba6ab8 Uploaded diff -r 327b2d99d4c5 -r f36b84d1ac09 README --- a/README Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -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 depends on the galaxy_protk and protk_trans_proteomic_pipeline packages -Please see instructions for those packages before installing. In particular -you will need to install system package requirements for galaxy_protk and protk_trans_proteomic_pipeline -using your package manager diff -r 327b2d99d4c5 -r f36b84d1ac09 mascot.xml --- a/mascot.xml Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,186 +0,0 @@ - - - - - galaxy_protk - - - Mascot MS/MS Search - - - rvm 1.9.3@protk-1.2.2 do 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 Search - - - diff -r 327b2d99d4c5 -r f36b84d1ac09 mascot_to_pepxml.xml --- a/mascot_to_pepxml.xml Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ - - - galaxy_protk - trans_proteomic_pipeline - - - Converts a mascot results file to pepXML - -rvm 1.9.3@protk-1.2.2 do 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 327b2d99d4c5 -r f36b84d1ac09 repository_dependencies.xml --- a/repository_dependencies.xml Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - - diff -r 327b2d99d4c5 -r f36b84d1ac09 tool-data/mascot_databases.loc.sample --- a/tool-data/mascot_databases.loc.sample Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#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 327b2d99d4c5 -r f36b84d1ac09 tool-data/mascot_mods.loc.sample --- a/tool-data/mascot_mods.loc.sample Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,77 +0,0 @@ -#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 327b2d99d4c5 -r f36b84d1ac09 tool-data/pepxml_databases.loc.sample --- a/tool-data/pepxml_databases.loc.sample Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#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_ diff -r 327b2d99d4c5 -r f36b84d1ac09 tool-data/tandem_mods.loc.sample --- a/tool-data/tandem_mods.loc.sample Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -#This file lists the names of inbuilt chemical modifications accepted by X!Tandem -# -# -Carbamidomethyl C carbamidomethyl_c_ 57.021464@C carbamidomethyl_c_ -Glycocapture-N glycocapture_n_ 0.998@N!{P}[ST] glycocapture_n_ -Oxidation M oxidation_m_ 15.994915@M oxidation_m_ \ No newline at end of file diff -r 327b2d99d4c5 -r f36b84d1ac09 tool_dependencies.xml --- a/tool_dependencies.xml Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ - - - - - - - - - - - -