protk 1.2.6.pre5 → 1.3.0.pre1

data/bin/mascot_to_pepxml.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 #
-# This file is part of MSLIMS
+# This file is part of Protk
 # Created by Ira Cooke 12/4/2010
 #
 # Convert mascot dat files to pepxml. A wrapper for Mascot2XML
@@ -15,34 +15,21 @@ require 'protk/mascot_util'
 #
 genv=Constants.new
 
-tool=SearchTool.new([:database,:explicit_output,:over_write,:enzyme])
+tool=SearchTool.new([
+  :database,
+  :explicit_output,
+  :over_write,
+  :enzyme])
+
 tool.option_parser.banner = "Convert mascot dat files to pep.xml files.\n\nUsage: mascot_to_pepxml.rb [options] file1.dat file2.dat ... "
 
 tool.options.enzyme="trypsin"
 
-tool.options.shortid=false
-tool.option_parser.on( '--shortid', 'Use short protein id as per Mascot result (default uses full protein ids in fasta file)' ) do  
-    tool.options.shortid=true
-end
-
-tool.option_parser.parse!
-
-exit unless tool.check_options 
-
-if ( ARGV[0].nil? )
-    puts "You must supply an input file"
-    puts tool.option_parser 
-    exit
-end
+tool.add_boolean_option(:shortid,false,['--shortid', 'Use short protein id as per Mascot result (default uses full protein ids in fasta file)' ])
 
-current_db=""
+exit unless tool.check_options(true,[:database])
 
-case 
-when Pathname.new(tool.database).exist? # It's an explicitly named db
-  current_db=Pathname.new(tool.database).realpath.to_s
-else
-  current_db=tool.current_database :fasta
-end
+database_path=tool.database_info.path
 
 
 
@@ -54,20 +41,20 @@ ARGV.each do |file_name|
   if ( tool.explicit_output==nil )
     new_basename="#{this_dir}/#{MascotUtil.input_basename(name)}_mascot2xml"      
     cmd="cp #{name} #{new_basename}.dat"
-    cmd << "; #{genv.mascot2xml} #{new_basename}.dat -D#{current_db} -E#{tool.enzyme}"
+    cmd << "; #{genv.mascot2xml} #{new_basename}.dat -D#{database_path} -E#{tool.enzyme}"
     
     cmd << " -shortid" if tool.shortid
 
   else  #Mascot2XML doesn't support explicitly named output files so we move the file to an appropriate output filename after finishing
     new_basename="#{this_dir}/#{MascotUtil.input_basename(name)}_mascot2xml"
     cmd="cp #{name} #{new_basename}.dat"
-    cmd << "; Mascot2XML #{new_basename}.dat -D#{current_db} -E#{tool.enzyme}"
+    cmd << "; Mascot2XML #{new_basename}.dat -D#{database_path} -E#{tool.enzyme}"
     cmd << " -shortid" if tool.shortid
     cmd << "; mv #{new_basename}.pep.xml #{tool.explicit_output}; rm #{new_basename}.dat"
     repair_script="#{File.dirname(__FILE__)}/repair_run_summary.rb"     
     cmd << "; #{repair_script} #{tool.explicit_output}"
   end
     
-  code = tool.run(cmd,genv,nil,nil)
+  code = tool.run(cmd,genv)
   throw "Command #{cmd} failed with exit code #{code}" unless code==0
 end

data/bin/msgfplus_search.rb

@@ -18,8 +18,19 @@ input_stager = nil
 
 # Setup specific command-line options for this tool. Other options are inherited from SearchTool
 #
-search_tool=SearchTool.new([:background,:database,:explicit_output,:over_write,:enzyme,
-  :modifications,:instrument,:mass_tolerance_units,:mass_tolerance,:cleavage_semi])
+search_tool=SearchTool.new([
+  :database,
+  :explicit_output,
+  :over_write,
+  :enzyme,
+  :modifications,
+  :methionine_oxidation,
+  :carbamidomethyl,
+  :glyco,
+  :acetyl_nterm,
+  :instrument,
+  :cleavage_semi,
+  :threads])
 
 search_tool.jobid_prefix="p"
 search_tool.option_parser.banner = "Run an MSGFPlus msms search on a set of msms spectrum input files.\n\nUsage: msgfplus_search.rb [options] file1.mzML file2.mzML ..."
@@ -28,73 +39,24 @@ search_tool.options.output_suffix="_msgfplus"
 search_tool.options.enzyme=1
 search_tool.options.instrument=0
 
-search_tool.options.no_pepxml=false
-search_tool.option_parser.on(  '--no-pepxml', 'Dont convert results to pepxml. Keep native mzidentml format' ) do
-  search_tool.options.no_pepxml=true
-end
-
-search_tool.options.isotope_error_range="0,1"
-search_tool.option_parser.on(  '--isotope-error-range range', 'Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation.(Default 0,1)' ) do |range|
-  search_tool.options.isotope_error_range=range
-end
-
-search_tool.options.fragment_method=0
-search_tool.option_parser.on(  '--fragment-method method', 'Fragment method 0: As written in the spectrum or CID if no info (Default), 1: CID, 2: ETD, 3: HCD, 4: Merge spectra from the same precursor' ) do |method|
-  search_tool.options.fragment_method=method
-end
-
-search_tool.options.protocol=0
-search_tool.option_parser.on(  '--protocol p', '0: NoProtocol (Default), 1: Phosphorylation, 2: iTRAQ, 3: iTRAQPhospho' ) do |p|
-  search_tool.options.protocol=p
-end
-
-search_tool.options.min_pep_length=6
-search_tool.option_parser.on(  '--min-pep-length p', 'Minimum peptide length to consider, Default: 6' ) do |p|
-  search_tool.options.min_pep_length=p
-end
-
-search_tool.options.max_pep_length=40
-search_tool.option_parser.on(  '--max-pep-length p', 'Maximum peptide length to consider, Default: 40' ) do |p|
-  search_tool.options.max_pep_length=p
-end
-
-search_tool.options.min_pep_charge=2
-search_tool.option_parser.on(  '--min-pep-charge c', 'Minimum precursor charge to consider if charges are not specified in the spectrum file, Default: 2' ) do |c|
-  search_tool.options.min_pep_charge=c
-end
-
-search_tool.options.max_pep_charge=3
-search_tool.option_parser.on(  '--max-pep-charge c', 'Maximum precursor charge to consider if charges are not specified in the spectrum file, Default: 3' ) do |c|
-  search_tool.options.max_pep_charge=c
-end
-
-search_tool.options.num_reported_matches=1
-search_tool.option_parser.on(  '--num-reported-matches n', 'Number of matches per spectrum to be reported, Default: 1' ) do |n|
-  search_tool.options.num_reported_matches=n
-end
-
-search_tool.options.add_features=false
-search_tool.option_parser.on(  '--add-features', 'output additional features' ) do 
-  search_tool.options.add_features=true
-end
-
-search_tool.options.num_threads=nil
-search_tool.option_parser.on('--threads NumThreads','Number of processing threads to use') do |nt|
-  search_tool.options.num_threads=nt
-end
-
-search_tool.options.java_mem="3500M"
-search_tool.option_parser.on('--java-mem mem','Java memory limit when running the search (Default 3.5Gb)') do |mem|
-  search_tool.options.java_mem=mem
-end
+# MS-GF+ doesnt support fragment tol so add this manually rather than via the SearchTool defaults
+search_tool.add_value_option(:precursor_tol,"20",['-p','--precursor-ion-tol tol', 'Precursor ion mass tolerance.'])
+search_tool.add_value_option(:precursor_tolu,"ppm",['--precursor-ion-tol-units tolu', 'Precursor ion mass tolerance units (ppm or Da). Default=ppm'])
+
+search_tool.add_boolean_option(:pepxml,false,['--pepxml', 'Convert results to pepxml.'])
+search_tool.add_value_option(:isotope_error_range,"0,1",['--isotope-error-range range', 'Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation.(Default 0,1)'])
+search_tool.add_value_option(:fragment_method,0,['--fragment-method method', 'Fragment method 0: As written in the spectrum or CID if no info (Default), 1: CID, 2: ETD, 3: HCD, 4: Merge spectra from the same precursor'])
+search_tool.add_boolean_option(:decoy_search,false,['--decoy-search', 'Build and search a decoy database on the fly. Input db should not contain decoys if this option is used'])
+search_tool.add_value_option(:protocol,0,['--protocol p', '0: NoProtocol (Default), 1: Phosphorylation, 2: iTRAQ, 3: iTRAQPhospho'])
+search_tool.add_value_option(:min_pep_length,6,['--min-pep-length p', 'Minimum peptide length to consider, Default: 6'])
+search_tool.add_value_option(:max_pep_length,40,['--max-pep-length p', 'Maximum peptide length to consider, Default: 40'])
+search_tool.add_value_option(:min_pep_charge,2,['--min-pep-charge c', 'Minimum precursor charge to consider if charges are not specified in the spectrum file, Default: 2'])
+search_tool.add_value_option(:max_pep_charge,3,['--max-pep-charge c', 'Maximum precursor charge to consider if charges are not specified in the spectrum file, Default: 3'])
+search_tool.add_value_option(:num_reported_matches,1,['--num-reported-matches n', 'Number of matches per spectrum to be reported, Default: 1'])
+search_tool.add_boolean_option(:add_features,false,['--add-features', 'output additional features'])
+search_tool.add_value_option(:java_mem,"3500M",['--java-mem mem','Java memory limit when running the search (Default 3.5Gb)'])
   
-exit unless search_tool.check_options 
-
-if ( ARGV[0].nil? )
-    puts "You must supply an input file"
-    puts search_tool.option_parser 
-    exit
-end
+exit unless search_tool.check_options(true)
 
 # Environment with global constants
 #
@@ -104,30 +66,34 @@ genv=Constants.new
 #
 msgf_bin="#{genv.msgfplusjar}"
 
-throw "Could not find MSGFPlus.jar" if (msgf_bin==nil) || (msgf_bin.length==0)
+# We need to cope with the fact that MSGFPlus.jar might not be executable so fall back to the protk predefined path
+
+msgf_bin = "#{genv.msgfplus_root}/MSGFPlus.jar " if !msgf_bin
+
+throw "Could not find MSGFPlus.jar" if !msgf_bin || (msgf_bin.length==0) || !File.exist?(msgf_bin)
 
 make_msgfdb_cmd=""
 
-case 
-when Pathname.new(search_tool.database).exist? # It's an explicitly named db
-  current_db=Pathname.new(search_tool.database).realpath.to_s
+@output_suffix="_msgfplus"
+@output_extension= search_tool.pepxml ? ".pep.xml" : ".mzid"
 
-  # Must have fasta extension
-  if ( Pathname.new(current_db).extname.to_s.downcase != ".fasta" )
-    make_msgfdb_cmd << "ln -s #{current_db} #{current_db}.fasta;"
-    current_db="#{current_db}.fasta"
-  end
+db_info=search_tool.database_info
 
-  if(not FileTest.exists?("#{current_db}.canno"))
-    dbdir = Pathname.new(current_db).dirname.realpath.to_s
-    make_msgfdb_cmd << "cd #{dbdir}; java -Xmx3500M -cp #{genv.msgfplusjar} edu.ucsd.msjava.msdbsearch.BuildSA -d #{current_db} -tda 0; "
-  end
-else
-  current_db=search_tool.current_database :fasta
+database_path=db_info.path
+
+# Database must have fasta extension
+if Pathname.new(database_path).extname.to_s.downcase != ".fasta"
+  make_msgfdb_cmd << "ln -s #{database_path} #{database_path}.fasta;"
+  database_path="#{database_path}.fasta"
+  db_info.path=database_path
 end
 
-fragment_tol = search_tool.fragment_tol
-precursor_tol = search_tool.precursor_tol
+# Database must be indexed
+unless FileTest.exists?("#{database_path}.canno")
+  dbdir = Pathname.new(database_path).dirname.realpath.to_s
+  tdavalue=search_tool.decoy_search ? 1 : 0;
+  make_msgfdb_cmd << "cd #{dbdir}; java -Xmx3500M -cp #{genv.msgfplusjar} edu.ucsd.msjava.msdbsearch.BuildSA -d #{database_path} -tda #{tdavalue}; "
+end
 
 
 throw "When --output is set only one file at a time can be run" if  ( ARGV.length> 1 ) && ( search_tool.explicit_output!=nil ) 
@@ -139,17 +105,12 @@ ARGV.each do |filename|
   if ( search_tool.explicit_output!=nil)
     output_path=search_tool.explicit_output
   else
-    output_path="#{search_tool.output_base_path(filename.chomp)}.pep.xml"
+    output_path=Tool.default_output_path(filename,@output_extension,search_tool.output_prefix,@output_suffix)
   end
 
 
-  # (*.mzML, *.mzXML, *.mgf, *.ms2, *.pkl or *_dta.txt)
-  # Get the input file extension
-  ext = Pathname.new(filename).extname
-  input_path="#{search_tool.input_base_path(filename.chomp)}#{ext}"
-
-  mzid_output_path="#{search_tool.input_base_path(filename.chomp)}.mzid"
-
+  input_path=filename.chomp
+  mzid_output_path="#{output_path}.mzid"
 
   if for_galaxy
     original_input_file = input_path
@@ -166,12 +127,17 @@ ARGV.each do |filename|
   
     # The basic command
     #
-    cmd= "#{make_msgfdb_cmd} java -Xmx#{search_tool.java_mem} -jar #{msgf_bin} -d #{current_db} -s #{input_path} -o #{mzid_output_path} "
+    cmd= "#{make_msgfdb_cmd} java -Xmx#{search_tool.java_mem} -jar #{msgf_bin} -d #{database_path} -s #{input_path} -o #{mzid_output_path} "
 
     #Semi tryptic peptides
     #
     cmd << " -ntt 1" if ( search_tool.cleavage_semi )
 
+    #Decoy searches
+    #
+    tdavalue=search_tool.decoy_search ? 1 : 0;
+    cmd << " -tda #{tdavalue}"
+
     # Precursor tolerance
     #
     cmd << " -t #{search_tool.precursor_tol}#{search_tool.precursor_tolu}"
@@ -203,7 +169,7 @@ ARGV.each do |filename|
 
     # Num Threads
     #
-    cmd << " -thread #{search_tool.num_threads}" if search_tool.num_threads
+    cmd << " -thread #{search_tool.threads}" if search_tool.threads > 0
 
     mods_file_content = ""
 
@@ -211,6 +177,9 @@ ARGV.each do |filename|
     #
     if ( search_tool.var_mods !="" && !search_tool.var_mods =~/None/) # Checking for none is to cope with galaxy input
       var_mods = search_tool.var_mods.split(",").collect { |mod| mod.lstrip.rstrip }.reject {|e| e.empty? }.join("\n")
+      var_mods << "O1,M,opt,any,Oxidation\n" if search_tool.methionine_oxidation
+      var_mods << "C2H2O,*,opt,Prot-N-term,Acetyl\n" if search_tool.acetyl_nterm
+      var_mods << "H-1N-1O1,N,opt,any,Deamidated\n" if search_tool.glyco      
       if ( var_mods !="" )
         mods_file_content << "#{var_mods}\n"
       end
@@ -220,13 +189,14 @@ ARGV.each do |filename|
   #
     if ( search_tool.fix_mods !="" && !search_tool.fix_mods=~/None/)
       fix_mods = search_tool.fix_mods.split(",").collect { |mod| mod.lstrip.rstrip }.reject { |e| e.empty? }.join("\n")
+      fix_mods << "C2H3N1O1,C,opt,any,Carbamidomethyl\n" if search_tool.carbamidomethyl
       if ( fix_mods !="")
         mods_file_content << "#{fix_mods}"    
       end
     end
 
     if ( mods_file_content != "")
-      mods_path="#{search_tool.input_base_path(filename.chomp)}.msgfplus_mods.txt"
+      mods_path="#{output_path}.msgfplus_mods.txt"
       mods_file=File.open(mods_path,'w+')
       mods_file.write "NumMods=2\n#{mods_file_content}"
       mods_file.close
@@ -234,15 +204,15 @@ ARGV.each do |filename|
     end
     
     # As a final part of the command we convert to pepxml
-    if search_tool.no_pepxml
-      cmd << "; cp #{mzid_output_path} #{output_path}"
-    else
+    if search_tool.pepxml
       #if search_tool.explicit_output
       cmd << ";ruby -pi.bak -e \"gsub('post=\\\"?','post=\\\"X')\" #{mzid_output_path}"
       cmd << ";ruby -pi.bak -e \"gsub('pre=\\\"?','pre=\\\"X')\" #{mzid_output_path}"
       cmd << ";idconvert #{mzid_output_path} --pepXML -o #{Pathname.new(mzid_output_path).dirname}" 
       #Then copy the pepxml to the final output path
       cmd << "; mv #{mzid_output_path.chomp('.mzid')}.pepXML #{output_path}"
+    else
+      cmd << "; mv #{mzid_output_path} #{output_path}"
     end
       
 
@@ -251,14 +221,7 @@ ARGV.each do |filename|
     
     # In case the user specified background running we need to create a jobscript path
     #
-    jobscript_path="#{output_path}.pbs.sh"
-
-    # Run the search
-    #
-    job_params= {:jobid => search_tool.jobid_from_filename(filename) }
-    job_params[:queue]="seventytwo"
-    job_params[:vmem]="70gb"
-    code = search_tool.run(cmd,genv,job_params,jobscript_path)
+    code = search_tool.run(cmd,genv)
     throw "Command failed with exit code #{code}" unless code==0
 
   if for_galaxy 

data/bin/omssa_search.rb

@@ -16,56 +16,37 @@ for_galaxy = GalaxyUtil.for_galaxy?
 
 # Setup specific command-line options for this tool. Other options are inherited from SearchTool
 #
-search_tool=SearchTool.new([:database,:explicit_output,:over_write,:enzyme,
-  :modifications,:instrument,:mass_tolerance_units,:mass_tolerance,:missed_cleavages,
-  :precursor_search_type,:respect_precursor_charges,:num_peaks_for_multi_isotope_search,:searched_ions
+search_tool=SearchTool.new([
+  :database,
+  :explicit_output,
+  :over_write,
+  :enzyme,
+  :modifications,
+  :methionine_oxidation,
+  :carbamidomethyl,
+  :glyco,
+  :instrument,
+  :mass_tolerance_units,
+  :mass_tolerance,
+  :missed_cleavages,
+  :precursor_search_type,
+  :respect_precursor_charges,
+  :num_peaks_for_multi_isotope_search,
+  :searched_ions,
+  :threads
   ])
 
 
 search_tool.option_parser.banner = "Run an OMSSA msms search on a set of mgf input files.\n\nUsage: omssa_search.rb [options] file1.mgf file2.mgf ..."
-search_tool.options.output_suffix="_omssa"
 
-search_tool.options.add_retention_times=true
-search_tool.option_parser.on( '-R', '--no-add-retention-times', 'Don\'t post process the output to add retention times' ) do 
-  search_tool.options.add_retention_times=false
-end
+search_tool.add_boolean_option(:add_retention_times,true,['-R', '--no-add-retention-times', 'Don\'t post process the output to add retention times'])
+search_tool.add_value_option(:max_hit_expect,1,['--max-hit-expect exp', 'Expect values less than this are considered to be hits'])
+search_tool.add_value_option(:intensity_cut_off,0.0005,['--intensity-cut-off co', 'Peak intensity cut-off as a fraction of maximum peak intensity'])
+search_tool.add_value_option(:galaxy_index_dir,nil,['--galaxy-index-dir dir', 'Specify galaxy index directory, will search for mods file there.'])
+search_tool.add_value_option(:omx_output,nil,['--omx-output path', 'Specify path for additional OMX output (optional).'])
+search_tool.add_value_option(:logfile,nil,['--logfile path','Send OMSSA stdout to a logfile'])
 
-search_tool.options.max_hit_expect=1
-search_tool.option_parser.on(  '--max-hit-expect exp', 'Expect values less than this are considered to be hits' ) do |exp|
-  search_tool.options.max_hit_expect=exp
-end
-
-search_tool.options.intensity_cut_off=0.0005
-search_tool.option_parser.on(  '--intensity-cut-off co', 'Peak intensity cut-off as a fraction of maximum peak intensity' ) do |co|
-  search_tool.options.intensity_cut_off=co
-end
-
-search_tool.options.galaxy_index_dir=nil
-search_tool.option_parser.on( '--galaxy-index-dir dir', 'Specify galaxy index directory, will search for mods file there.' ) do |dir|
-  search_tool.options.galaxy_index_dir=dir
-end
-
-search_tool.options.omx_output=nil
-search_tool.option_parser.on( '--omx-output path', 'Specify path for additional OMX output (optional).' ) do |path|
-  search_tool.options.omx_output=path
-end
-
-if ( ENV['PROTK_OMSSA_NTHREADS'] )
-  search_tool.options.nthreads=ENV['PROTK_OMSSA_NTHREADS']
-else
-  search_tool.options.nthreads=0
-end
-search_tool.option_parser.on( '--nthreads num', 'Number of search threads to use. Default is to use the value in environment variable PROTK_OMSSA_NTHREADS or else to autodetect' ) do |num|
-  search_tool.options.nthreads=num
-end
-
-exit unless search_tool.check_options 
-
-if ( ARGV[0].nil? )
-    puts "You must supply an input file"
-    puts search_tool.option_parser 
-    exit
-end
+exit unless search_tool.check_options(true)
 
 # Environment with global constants
 #
@@ -73,24 +54,18 @@ genv=Constants.new
 
 # Set search engine specific parameters on the SearchTool object
 #
-rt_correct_bin="#{File.dirname(__FILE__)}/correct_omssa_retention_times.rb"
 repair_script_bin="#{File.dirname(__FILE__)}/repair_run_summary.rb"
 
 make_blastdb_cmd=""
+@output_suffix="_omssa"
 
-case 
-when Pathname.new(search_tool.database).exist? # It's an explicitly named db
-  current_db=Pathname.new(search_tool.database).realpath.to_s
-  if(not FileTest.exists?("#{current_db}.phr"))
-    make_blastdb_cmd << "makeblastdb -dbtype prot -parse_seqids -in #{current_db}; "
-  end
-else
-  current_db=search_tool.current_database :fasta
-end
-
-fragment_tol = search_tool.fragment_tol
-precursor_tol = search_tool.precursor_tol
+db_info = search_tool.database_info
 
+# Index the DB if needed
+#
+unless File.exists?("#{db_info.path}.phr")
+  make_blastdb_cmd << "makeblastdb -dbtype prot -parse_seqids -in #{db_info.path}; "
+end
 
 throw "When --output is set only one file at a time can be run" if  ( ARGV.length> 1 ) && ( search_tool.explicit_output!=nil ) 
 
@@ -101,18 +76,10 @@ ARGV.each do |filename|
   if ( search_tool.explicit_output!=nil)
     output_path=search_tool.explicit_output
   else
-    output_path="#{search_tool.output_base_path(filename.chomp)}.pep.xml"
+    output_path=Tool.default_output_path(filename,".pep.xml",search_tool.output_prefix,@output_suffix)
   end
   
-  # We always perform searches on mgf files so 
-  #
-  input_path="#{search_tool.input_base_path(filename.chomp)}.mgf"
-  input_ext=Pathname.new(filename).extname
-
-  if ( input_ext==".dat" )
-    # This is a file provided by galaxy so we need to leave the .dat extension
-    input_path="#{search_tool.input_base_path(filename.chomp)}.dat"
-  end
+  input_path=filename.chomp
 
 
   # Only proceed if the output file is not present or we have opted to over-write it
@@ -121,7 +88,7 @@ ARGV.each do |filename|
   
     # The basic command
     #
-    cmd = "#{make_blastdb_cmd} omssacl -nt #{search_tool.nthreads} -d #{current_db} -fm #{input_path} -op #{output_path} -w"
+    cmd = "#{make_blastdb_cmd} omssacl -nt #{search_tool.threads} -d #{db_info.path} -fm #{input_path} -op #{output_path} -w"
 
     #Missed cleavages
     #
@@ -157,7 +124,7 @@ ARGV.each do |filename|
     
     # Fragment ion tolerance
     #
-    cmd << " -to #{fragment_tol}" #Always in Da
+    cmd << " -to #{search_tool.fragment_tol}" #Always in Da
     
     # Set the search type (monoisotopic vs average masses) and whether to use strict monoisotopic masses
     #
@@ -179,38 +146,24 @@ ARGV.each do |filename|
 
     # Variable Modifications
     #
-    if ( search_tool.var_mods !="" && !(search_tool.var_mods =~/None/)) # Checking for none is to cope with galaxy input
-      var_mods = search_tool.var_mods.split(",").collect { |mod| mod.lstrip.rstrip }.reject {|e| e.empty? }.join(",")
-
-      if ( var_mods !="" )
-        cmd << " -mv #{var_mods}"
-      end
-    else 
-      # Add options related to peptide modifications
-      #
-      if ( search_tool.glyco )
-        cmd << " -mv 119 "
-      end
+    if ( search_tool.var_mods  && !(search_tool.var_mods =~/None/)) # Checking for none is to cope with galaxy input
+      var_mods = search_tool.var_mods.split(",").collect { |mod| mod.lstrip.rstrip }.reject {|e| e.empty? }
     end
 
-    if ( search_tool.fix_mods !="" && !(search_tool.fix_mods=~/None/))
-      fix_mods = search_tool.fix_mods.split(",").collect { |mod| mod.lstrip.rstrip }.reject { |e| e.empty? }.join(",")
-      if ( fix_mods !="")
-        cmd << " -mf #{fix_mods}"    
-      end
-    else
-      if ( search_tool.has_modifications )
-        cmd << " -mf "
-        if ( search_tool.carbamidomethyl )
-          cmd<<"3 "
-        end
+    var_mods=[] unless var_mods
+    var_mods << "119" if search_tool.glyco
+    var_mods << "1" if search_tool.methionine_oxidation
 
-        if ( search_tool.methionine_oxidation )
-          cmd<<"1 "
-        end
+    cmd << " -mv #{var_mods.join(",")}" if var_mods.length > 0
 
-      end
+
+    if ( search_tool.fix_mods  && !(search_tool.fix_mods=~/None/))
+      fix_mods = search_tool.fix_mods.split(",").collect { |mod| mod.lstrip.rstrip }.reject { |e| e.empty? }
     end
+    fix_mods=[] unless fix_mods
+    fix_mods << ["3"] if search_tool.carbamidomethyl
+
+    cmd << " -mf #{fix_mods.join(",")}" if fix_mods.length > 0
     
     if ( search_tool.searched_ions !="" && !(search_tool.searched_ions=~/None/))
       searched_ions=search_tool.searched_ions.split(",").collect{ |mod| mod.lstrip.rstrip }.reject { |e| e.empty? }.join(",")
@@ -235,29 +188,19 @@ ARGV.each do |filename|
     cmd << " -ci #{search_tool.intensity_cut_off}"
     
     # Send output to logfile. OMSSA Logging does not play well with Ruby Open4
-    cmd << " -logfile omssa.log"
+    cmd << " -logfile #{search_tool.logfile}" if search_tool.logfile
 
     # Up to here we've formulated the omssa command. The rest is cleanup
     p "Running:#{cmd}"
     
-    # Add retention time corrections
-    #
-    if (search_tool.options.add_retention_times)
-      # TODO: Really correct rts
-#      cmd << "; #{rt_correct_bin} #{output_path} #{input_path} "
-    end
     
     # Correct the pepXML file 
     #
-#    cmd << "; #{repair_script_bin} -N #{input_path} -R mgf #{output_path} --omssa-itol #{search_tool.fragment_tol}"
-#    genv.log("Running repair script command #{cmd}",:info)
+   cmd << "; #{repair_script_bin} -N #{input_path} -R mgf #{output_path} --omssa-itol #{search_tool.fragment_tol}"
     
     # Run the search
     #
-    job_params= {:jobid => search_tool.jobid_from_filename(filename) }
-    job_params[:queue]="lowmem"
-    job_params[:vmem]="900mb"    
-    search_tool.run(cmd,genv,job_params)
+    search_tool.run(cmd,genv)
 
 
   else