# HG changeset patch # User iracooke # Date 1362450992 18000 # Node ID e3ed58461b7dfed48c737bb9ce3e2934c06816d7 # Parent f40325a78a99a65f68f87c726540de4cabef12c7 Uploaded diff -r f40325a78a99 -r e3ed58461b7d README --- a/README Mon Mar 04 20:54:11 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -This package is a galaxy wrapper for the MSGF+ search tool. - -The underlying MSGF+ tool itself should be automatically installed however you must -satisfy the requirements below before attempting to install. - -System Requirements. Ensure that you have the following packages installed on your system - -(For protk_msgfplus) -- unzip -- java runtime 6 or higher - -(For galaxy_protk) -- The ability to download files (an internet connection): curl wget -- gcc g++ make autoconf automake libtool pkg-config patch git openssl -libreadline6 libreadline6-dev git-core zlib1g zlib1g-dev libssl-dev -libc6-dev ncurses-dev bison subversion libxml2 libxml2-dev diff -r f40325a78a99 -r e3ed58461b7d msgfplus_search.xml --- a/msgfplus_search.xml Mon Mar 04 20:54:11 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,140 +0,0 @@ - - - - galaxy_protk - msgfplus - proteowizard - - - - Run an MSGF+ Search - - - #if $database.source_select=="built_in": - rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb --galaxy -d $database.dbkey - #else #rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb -d $database.fasta_file - #end if - - --var-mods=' - $variable_mods - #for $custom_variable_mod in $custom_variable_mods: - ,${custom_variable_mod.custom_mod} - #end for - ' - - --fix-mods=' - $fixed_mods - #for $custom_fix_mod in $custom_fix_mods: - ,${custom_fix_mod.custom_mod} - #end for - ' - - $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol --instrument=$instrument - - - - - - - - - - - - - - Database - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Missed Cleavages Allowed - - - - - - - Enzyme - - - - - Instrument Type - - - - - - - - - - Precursor Ion Tolerance Units - - - - - - - - - - - - - - -**What it does** - -Runs an MS/MS database search using the MSGFPlus search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores. - ----- - -**References** - -Please see http://proteomics.ucsd.edu/Software/MSGFPlus.html for details of the MSGFPlus search engine and references describing its algorithm - - - - diff -r f40325a78a99 -r e3ed58461b7d repository_dependencies.xml --- a/repository_dependencies.xml Mon Mar 04 20:54:11 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ - - - - - - - - - - - - diff -r f40325a78a99 -r e3ed58461b7d tool-data/msgfplus_mods.loc.sample --- a/tool-data/msgfplus_mods.loc.sample Mon Mar 04 20:54:11 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ -#This file lists the names of inbuilt chemical modifications accepted by msgfplus -#Each entry consists of 4 tab separated fields like this -# -# -#Modification strings should conform to the standard MSGFPlus syntax with the following exception -#The ModType field is overridden by the msgfplus_search.rb tool. In other words any of these mods -#May be passed to the tool as a variable or fixed mod and the tool will substitute the appropriate ModType -#value -# -#Standard MSGFPlus syntax is -# -# To input a modification, use the following command: -# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required). -# CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num]) -# - C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed. -# - Atom can be omitted. The sequence of atoms must be followed. -# - Negative numbers are allowed. -# - E.g. C2H2O1 (valid), H2C1O1 (invalid) -# Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient). -# - E.g. 15.994915 -# Residues: affected amino acids (must be upper letters) -# - Must be uppor letters or * -# - Use * if this modification is applicable to any residue. -# - * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.) -# - E.g. NQ, * -# ModType: "fix" for fixed modifications, "opt" for variable modifications (case insensitive) -# Position: position in the peptide where the modification can be attached. -# - One of the following five values should be used: -# - any (anywhere), N-term (peptide N-term), C-term (peptide C-term), Prot-N-term (protein N-term), Prot-C-term (protein C-term) -# - Case insensitive -# - "-" can be omitted -# - E.g. any, Any, Prot-n-Term, ProtNTerm => all valid -# Name: name of the modification (Unimod PSI-MS name) -# - For proper mzIdentML output, this name should be the same as the Unimod PSI-MS name -# - E.g. Phospho, Acetyl -#C2H3N1O1,C,fix,any,Carbamidomethyl # Fixed Carbamidomethyl C -# Variable Modifications (default: none) -#O1,M,opt,any,Oxidation # Oxidation M -#15.994915,M,opt,any,Oxidation # Oxidation M (mass is used instead of CompositionStr) -#H-1N-1O1,NQ,opt,any,Deamidated # Negative numbers are allowed. -#C2H3NO,*,opt,N-term,Carbamidomethyl # Variable Carbamidomethyl N-term -#H-2O-1,E,opt,N-term,Pyro_glu # Pyro-glu from E -#H-3N-1,Q,opt,N-term,Pyro-glu # Pyro-glu from Q -#C2H2O,*,opt,Prot-N-term,Acetyl # Acetylation Protein N-term -#C2H2O1,K,opt,any,Acetyl # Acetylation K -#CH2,K,opt,any,Methy # Methylation K -#HO3P,STY,opt,any,Phospho # Phosphorylation STY - -Carbamidomethyl C carbamidomethyl_c_ C2H3N1O1,C,opt,any,Carbamidomethyl carbamidomethyl_c_ -Oxidation M oxidation_m_ O1,M,opt,any,Oxidation oxidation_m_ \ No newline at end of file diff -r f40325a78a99 -r e3ed58461b7d tool-data/pepxml_databases.loc.sample --- a/tool-data/pepxml_databases.loc.sample Mon Mar 04 20:54:11 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_ spall 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 f40325a78a99 -r e3ed58461b7d tool_dependencies.xml --- a/tool_dependencies.xml Mon Mar 04 20:54:11 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ - - - - - - - - - - - - - - - - - \ No newline at end of file