# HG changeset patch # User iracooke # Date 1362448084 18000 # Node ID 0d21fdb9c999468b808687487d355711497c4e47 # Parent 528bcbb94199c2d8741a23a15f52141b18bd6c48 Uploaded diff -r 528bcbb94199 -r 0d21fdb9c999 README --- a/README Mon Mar 04 20:06:45 2013 -0500 +++ b/README Mon Mar 04 20:48:04 2013 -0500 @@ -1,6 +1,16 @@ -This package is an installer for the MSGF+ search tool. +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 528bcbb94199 -r 0d21fdb9c999 msgfplus_search.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msgfplus_search.xml Mon Mar 04 20:48:04 2013 -0500 @@ -0,0 +1,140 @@ + + + + galaxy_protk + msgfplus + + + + + 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 528bcbb94199 -r 0d21fdb9c999 repository_dependencies.xml --- a/repository_dependencies.xml Mon Mar 04 20:06:45 2013 -0500 +++ b/repository_dependencies.xml Mon Mar 04 20:48:04 2013 -0500 @@ -1,10 +1,10 @@ - + + + + - - - \ No newline at end of file + + + diff -r 528bcbb94199 -r 0d21fdb9c999 tool-data/msgfplus_mods.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/msgfplus_mods.loc.sample Mon Mar 04 20:48:04 2013 -0500 @@ -0,0 +1,50 @@ +#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 528bcbb94199 -r 0d21fdb9c999 tool-data/pepxml_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pepxml_databases.loc.sample Mon Mar 04 20:48:04 2013 -0500 @@ -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_ 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 528bcbb94199 -r 0d21fdb9c999 tool_dependencies.xml --- a/tool_dependencies.xml Mon Mar 04 20:06:45 2013 -0500 +++ b/tool_dependencies.xml Mon Mar 04 20:48:04 2013 -0500 @@ -1,23 +1,17 @@ - - - - https://dl.dropbox.com/u/226794/galaxy_protk.tar.gz - sh install_msgfplus.sh $INSTALL_DIR 1.1.9 - - install_msgfplus.sh - $INSTALL_DIR - - - $INSTALL_DIR - $INSTALL_DIR - - - - - Installs MSGF+ via the protk installer - + + + + + + + + + + + + \ No newline at end of file