# 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
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-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
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- galaxy_protk
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- Mascot MS/MS Search
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- rvm 1.9.3@protk-1.2.2 do mascot_search.rb
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- #if $database.source_select=="built_in":
- -d $database.dbkey
- #else
- -d $database.custom_db
- #end if
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- -f $fragment_ion_tol
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- -S $server $input_file
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- -o $output
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- -r
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- ## Variable Mods
-
- --var-mods='
- $variable_mods
- '
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- --fix-mods='
- $fixed_mods
- '
- --allowed-charges=$allowed_charges
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- --enzyme=$enzyme
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- --instrument=$instrument
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- --precursor-ion-tol-units=$precursor_tolu
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- --email=$email
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- -v $missed_cleavages
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- #if $security.security_use
- --use-security
- --username $security.username
- --password $security.password
- #end if
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- #if $proxy
- --proxy $proxy
- #end if
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- Run a Mascot Search
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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 @@
-
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- galaxy_protk
- trans_proteomic_pipeline
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- 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
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- $shortid
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- Convert mascot results from mascotdat to pepXML
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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 @@
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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
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