# HG changeset patch # User iracooke # Date 1362432498 18000 # Node ID 579b1f9146b432ff52fdb871dbbbee8d06f3230f # Parent cd2955b6646f78cc8af80a3b43dd4f64c3a65cab Uploaded diff -r cd2955b6646f -r 579b1f9146b4 mascot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mascot.xml Mon Mar 04 16:28:18 2013 -0500 @@ -0,0 +1,135 @@ + + + + + galaxy_protk + + + Run a Mascot Search on a File + + + rvm 1.9.3@protk-1.1.9 do mascot_search.rb -d $database -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 --username=$username -v $missed_cleavages + + + + + + + + + Database + + + + + + + + + + + + + + + + + + + + + + + + Missed Cleavages Allowed + + + + + + + Enzyme + + + + + Peptide Charge + + + + + + + + + + + + + + + + + + + + + + + + + + + Instrument + + + + + + + + + + + + + + + + + + + + Precursor Ion Tolerance Units + + + + + + + + + + + + + + + + + Run a Mascot Search + + + diff -r cd2955b6646f -r 579b1f9146b4 mascot_to_pepxml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mascot_to_pepxml.xml Mon Mar 04 16:28:18 2013 -0500 @@ -0,0 +1,31 @@ + + + galaxy_protk + trans_proteomic_pipeline + + + Converts a mascot results file to pepXML + +rvm 1.9.3@protk-1.1.9 do mascot_to_pepxml.rb $input_file -o $output -d $database + + + + + Database + + + + + + + + + + + + + + Convert mascot results from mascotdat to pepXML + + + diff -r cd2955b6646f -r 579b1f9146b4 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Mar 04 16:28:18 2013 -0500 @@ -0,0 +1,10 @@ + + + + + + + + + + diff -r cd2955b6646f -r 579b1f9146b4 tool-data/mascot_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mascot_databases.loc.sample Mon Mar 04 16:28:18 2013 -0500 @@ -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_ SPAll spall_ +Swissprot Human sphuman_ SPHuman sphuman_ \ No newline at end of file diff -r cd2955b6646f -r 579b1f9146b4 tool-data/mascot_mods.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mascot_mods.loc.sample Mon Mar 04 16:28:18 2013 -0500 @@ -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 cd2955b6646f -r 579b1f9146b4 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Mar 04 16:28:18 2013 -0500 @@ -0,0 +1,12 @@ + + + + + + + + + + + + \ No newline at end of file