# HG changeset patch # User iracooke # Date 1343017003 14400 # Node ID deaedec14cc8566c3cd97469b55f2501e5655707 # Parent a929e27eb20395d454f80882b783a6296408d2ce Improved help text to include proper citations diff -r a929e27eb203 -r deaedec14cc8 display_applications/proteomics/PepXml.xml --- a/display_applications/proteomics/PepXml.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ - - - - - - - ${site_url}/init_local?file=${encoded_filename.qp}&type=pepxml - - - - #import binascii - ${binascii.hexlify( $pepxml_file.file_name )} - - - ${BASE_URL.split(":")[1][2:]} - - - diff -r a929e27eb203 -r deaedec14cc8 display_applications/proteomics/ProtXml.xml --- a/display_applications/proteomics/ProtXml.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ - - - - - - - ${site_url}/init_local?file=${encoded_filename.qp}&type=protxml - - - - #import binascii - ${binascii.hexlify( $protxml_file.file_name )} - - - ${BASE_URL.split(":")[1][2:]} - - - \ No newline at end of file diff -r a929e27eb203 -r deaedec14cc8 display_applications/proteomics/mzML.xml --- a/display_applications/proteomics/mzML.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ - - - - - - - ${site_url}/init_local?file=${encoded_filename.qp}&type=mzml - - - - #import binascii - ${binascii.hexlify( $mzml_file.file_name )} - - - ${BASE_URL.split(":")[1][2:]} - - - \ No newline at end of file diff -r a929e27eb203 -r deaedec14cc8 interprophet.xml --- a/interprophet.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ - - protk - Combine Peptide Prophet results from multiple search engines - - - - interprophet_wrapper.rb $output $use_nss $use_nrs $use_nse $use_nsi $use_nsm --minprob $minprob - - - ## Inputs. - ${first_input} - #for $input_file in $input_files: - ${input_file.additional_input} - #end for - - - - - - - - - - - - - - - - - - - - - - - - - - Run InterProphet - - - diff -r a929e27eb203 -r deaedec14cc8 interprophet_wrapper.rb --- a/interprophet_wrapper.rb Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -require 'pathname' - -$VERBOSE=nil - -# Hard-Coded argument order and number of arguments -# -actual_output_path_string=ARGV[0] -use_nss=ARGV[1] -use_nrs=ARGV[2] -use_nse=ARGV[3] -use_nsi=ARGV[4] -use_nsm=ARGV[5] -minprob=ARGV[6] -minprob_val=ARGV[7] - -wd= Dir.pwd -original_input_files=ARGV.drop(7) -# End hard coded args # - -cmd="" - -output_substitution_cmds="" - -input_files=original_input_files.collect do |input| - - # We append ".pep.xml" to the input file name because interprophet can't handle anything else - # In order for this to work properly we need to create a symbolic link our working directory - # - original_input_path=Pathname.new("#{input}") - actual_input_path_string="#{wd}/#{original_input_path.basename}.pep.xml" - - cmd << "ln -s #{input} #{actual_input_path_string};" - output_substitution_cmds << "ruby -pi -e \"gsub('#{actual_input_path_string}', '#{input}.pep.xml')\" interprophet_output.pep.xml;" - actual_input_path_string -end - -interprophet_path=%x[which interprophet.rb] -cmd << interprophet_path.chomp - -cmd << " --no-nss" unless use_nss=="blank" -cmd << " --no-nrs" unless use_nrs=="blank" -cmd << " --no-nse" unless use_nse=="blank" -cmd << " --no-nsi" unless use_nsi=="blank" -cmd << " --no-nsm" unless use_nsm=="blank" - - -input_files.each { |input| - cmd << " #{input}" -} - - -cmd << " -o interprophet_output.pep.xml -r" - -cmd << ";#{output_substitution_cmds}" - -%x[#{cmd}] - diff -r a929e27eb203 -r deaedec14cc8 lib/galaxy/datatypes/proteomics.py --- a/lib/galaxy/datatypes/proteomics.py Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,181 +0,0 @@ -""" -Proteomics format classes -""" -import logging -import re -from galaxy.datatypes.data import * -from galaxy.datatypes.xml import * -from galaxy.datatypes.sniff import * -from galaxy.datatypes.binary import * - -log = logging.getLogger(__name__) - - -class Xls( Binary ): - """Class describing a binary excel spreadsheet file""" - file_ext = "xls" - - def set_peek( self, dataset, is_multi_byte=False ): - if not dataset.dataset.purged: - dataset.peek = "Excel Spreadsheet file" - dataset.blurb = data.nice_size( dataset.get_size() ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def display_peek( self, dataset ): - try: - return dataset.peek - except: - return "Binary xls file (%s)" % ( data.nice_size( dataset.get_size() ) ) - -class PepXml(GenericXml): - """pepXML data""" - file_ext = "pepxml" - - def set_peek( self, dataset, is_multi_byte=False ): - """Set the peek and blurb text""" - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) - dataset.blurb = 'pepXML data' - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def sniff( self, filename ): - """ - Determines whether the file is pepXML - """ - #TODO - Use a context manager on Python 2.5+ to close handle - handle = open(filename) - xmlns_re = re.compile(".*pepXML\"") - for i in range(3): - line = handle.readline() - if xmlns_re.match(line.strip()): - handle.close() - return True - - handle.close() - return False - -class MzML( GenericXml ): - """mzML data""" - file_ext = "mzml" - - def set_peek( self, dataset, is_multi_byte=False ): - """Set the peek and blurb text""" - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) - dataset.blurb = 'mzML Mass Spectrometry data' - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - - def sniff( self, filename ): - handle = open(filename) - xmlns_re = re.compile("^', - 'xmlns="http://regis-web.systemsbiology.net/protXML"' ] - - for i, line in enumerate( file( filename ) ): - if i >= len( pepxml_header ): - return True - line = line.rstrip( '\n\r' ) - if protxml_header[ i ] not in line: - return False - - - -class MzXML( Text ): - """mzXML data""" - file_ext = "mzXML" - - def set_peek( self, dataset, is_multi_byte=False ): - """Set the peek and blurb text""" - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) - dataset.blurb = 'mzXML Mass Spectrometry data' - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def sniff( self, filename ): - mzxml_header = [ '', - '' ] - for i, line in enumerate( file( filename ) ): - if i >= len( mzxml_header ): - return True - line = line.rstrip( '\n\r' ) - if line != mzxml_header[ i ]: - return False - -class Mgf( Text ): - """Mascot Generic Format data""" - file_ext = "mgf" - - def set_peek( self, dataset, is_multi_byte=False ): - """Set the peek and blurb text""" - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) - dataset.blurb = 'mgf Mascot Generic Format' - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - - - def sniff( self, filename ): - mgf_begin_ions = "BEGIN IONS" - max_lines=100 - - for i, line in enumerate( file( filename ) ): - line = line.rstrip( '\n\r' ) - if line==mgf_begin_ions: - return True - if i>max_lines: - return False - - -class MascotDat( Text ): - """Mascot search results """ - file_ext = "mascotdat" - - def set_peek( self, dataset, is_multi_byte=False ): - """Set the peek and blurb text""" - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) - dataset.blurb = 'mascotdat Mascot Search Results' - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - - - def sniff( self, filename ): - mime_version = "MIME-Version: 1.0 (Generated by Mascot version 1.0)" - max_lines=10 - - for i, line in enumerate( file( filename ) ): - line = line.rstrip( '\n\r' ) - if line==mime_version: - return True - if i>max_lines: - return False diff -r a929e27eb203 -r deaedec14cc8 make_decoy.xml --- a/make_decoy.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ - - - protk - - - Creates a random protein database with similar properties to a real protein database - - make_decoy.rb $input_file -o $output -L $length -P $prefix $append - - - - - - - - - - - - - - - Create random protein sequences - - - diff -r a929e27eb203 -r deaedec14cc8 mzml_to_mgf.xml --- a/mzml_to_mgf.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ - - - protk - - - Converts an mzML file to mgf suitable for searching by omssa - - file_convert.rb $input_file -o $output $maldi - - - - - - - - - - - - - - Convert line spectra to Mascot Generic Format - - - diff -r a929e27eb203 -r deaedec14cc8 omssa.xml --- a/omssa.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,150 +0,0 @@ - - - protk - - - Run an OMSSA MS/MS Search - - #if $database.source_select=="built_in": - omssa_search.rb -d $database.dbkey - #else #omssa_search.rb -d $database.fasta_file - #end if - - --var-mods=' - $variable_mods - ' - - --fix-mods=' - $fixed_mods - ' - - --searched-ions=' - $searched_ions - ' - - $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol --num-peaks-for-multi-isotope-search $multi_isotope $use_average_mass $respect_precursor_charges --max-hit-expect $max_hit_expect --intensity-cut-off $intensity_cut_off - - - - - - - - - - - - - Database - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Missed Cleavages Allowed - - - - - - - Enzyme - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Precursor Ion Tolerance Units - - - - - - - - - Multi-isotope search. - - - - - - - - - - - - - - - - - - - - - - - - - - - Run an OMSSA Search - - diff -r a929e27eb203 -r deaedec14cc8 peptide_prophet.xml --- a/peptide_prophet.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ - - protk - Calculate Peptide Prophet statistics on search results - - peptide_prophet_wrapper.rb ${output} ${input_file} -r $glyco $useicat $phospho $usepi $usert $accurate_mass $no_ntt $no_nmc $use_gamma $use_only_expect $force_fit $allow_alt_instruments $maldi - - - - - - - - - - - - - - - - - - - - - - - - - - - - Run Peptide Prophet - - - - - - diff -r a929e27eb203 -r deaedec14cc8 peptide_prophet_wrapper.rb --- a/peptide_prophet_wrapper.rb Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -require 'pathname' - -$VERBOSE=nil - -peptide_prophet_path=%x[which peptide_prophet.rb] - -actual_output_path_string=ARGV.shift - -# Second argument is the original input file name ... we'll change this below -original_input_file=ARGV[0] - -# Before doing anything we append create a link to the input file in our working dir with ".pep.xml" appended to the input -# name because peptide prophet can't handle anything else - -wd= Dir.pwd - -original_input_path=Pathname.new("#{original_input_file}") -actual_input_path_string="#{wd}/#{original_input_path.basename}.pep.xml" -full_tmp_output_path_string="#{wd}/peptide_prophet_output.pep.xml" - -cmd = "ln -s #{original_input_file} #{actual_input_path_string};" - -cmd << peptide_prophet_path.chomp - - -ARGV[0]="#{actual_input_path_string}" - -ARGV.each { |a| - cmd << " #{a}" -} - -cmd << " -o peptide_prophet_output.pep.xml" - -# Finally we need to fix up the output file so any references to the temporary working file are changed to refs to the original input file -cmd << ";ruby -pi -e \"gsub('#{actual_input_path_string}', '#{original_input_file}')\" peptide_prophet_output.pep.xml" -cmd << ";ruby -pi -e \"gsub('#{full_tmp_output_path_string}', '#{actual_output_path_string}')\" peptide_prophet_output.pep.xml" - -%x[#{cmd}] diff -r a929e27eb203 -r deaedec14cc8 pepxml_to_table.xml --- a/pepxml_to_table.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ - - protk - Converts a pepXML file to a tab delimited text file - - - -pepxml_to_table.rb $input_file -o $output - - - - - - - - - - - - - Convert a pepXML file to Tab delimited text - - - diff -r a929e27eb203 -r deaedec14cc8 protein_prophet.xml --- a/protein_prophet.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ - - protk - Calculate Protein Prophet statistics on search results - - - - protein_prophet_wrapper.rb $output $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Run Peptide Prophet - - - diff -r a929e27eb203 -r deaedec14cc8 protein_prophet_wrapper.rb --- a/protein_prophet_wrapper.rb Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -require 'pathname' - -$VERBOSE=nil - -protein_prophet_path=%x[which protein_prophet.rb] - -actual_output_path_string=ARGV.shift - -# Second argument is the original input file name ... we'll change this below -original_input_file=ARGV[0] - -# Before doing anything we append create a link to the input file in our working dir with ".pep.xml" appended to the input -# name because peptide prophet can't handle anything else - -wd= Dir.pwd - -original_input_path=Pathname.new("#{original_input_file}") -actual_input_path_string="#{wd}/#{original_input_path.basename}.pep.xml" - -cmd = "ln -s #{original_input_file} #{actual_input_path_string};" - -cmd << protein_prophet_path.chomp - - -ARGV[0]="#{actual_input_path_string}" - -ARGV.each { |a| - - cmd << " #{a}" -} - -cmd << " -o protein_prophet_results.prot.xml" - -cmd << ";ruby -pi -e \"gsub('#{actual_input_path_string}', '#{original_input_file}.pep.xml')\" protein_prophet_results.prot.xml" - -%x[#{cmd}] - diff -r a929e27eb203 -r deaedec14cc8 tandem.xml --- a/tandem.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,118 +0,0 @@ - - protk - Run an X!Tandem Search - - - #if $database.source_select=="built_in": - tandem_search.rb -d $database.dbkey - #else #tandem_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 $allow_multi_isotope_search --keep-params-files - - - - - - - - - - - - - - Database - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Missed Cleavages Allowed - - - - - - - Enzyme - - - - - - - - Precursor Ion Tolerance Units - - - - - - - - - - - - - - - - Run an X!Tandem Search - - - diff -r a929e27eb203 -r deaedec14cc8 tool-data/datatypes_conf.xml --- a/tool-data/datatypes_conf.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r a929e27eb203 -r deaedec14cc8 tool-data/mascot_databases.loc.sample --- a/tool-data/mascot_databases.loc.sample Thu Jun 21 22:30:48 2012 -0400 +++ /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_ SPAll spall_ -Swissprot Human sphuman_ SPHuman sphuman_ \ No newline at end of file diff -r a929e27eb203 -r deaedec14cc8 tool-data/mascot_mods.loc.sample --- a/tool-data/mascot_mods.loc.sample Thu Jun 21 22:30:48 2012 -0400 +++ /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 a929e27eb203 -r deaedec14cc8 tool-data/omssa_mods.loc.sample --- a/tool-data/omssa_mods.loc.sample Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,181 +0,0 @@ -#This file lists the names of chemical modifications accepted by OMMSA -# -# -2-amino-3-oxo-butanoic acid T 2-amino-3-oxo-butanoicacidt_ 23 2-amino-3-oxo-butanoicacidt_ -Asparagine HexNAc asparaginehexnac_ 182 asparaginehexnac_ -Asparagine dHexHexNAc asparaginedhexhexnac_ 183 asparaginedhexhexnac_ -CAMthiopropanoyl K camthiopropanoylk_ 131 camthiopropanoylk_ -CHD2-di-methylation of K chd2-di-methylationofk_ 189 chd2-di-methylationofk_ -CHD2-di-methylation of peptide n-term chd2-di-methylationofpeptiden-term_ 190 chd2-di-methylationofpeptiden-term_ -ICAT heavy icatheavy_ 130 icatheavy_ -ICAT light icatlight_ 129 icatlight_ -M cleavage from protein n-term mcleavagefromproteinn-term_ 9 mcleavagefromproteinn-term_ -MMTS on C mmtsonc_ 179 mmtsonc_ -Maleimide-PEO2-Biotin of C maleimide-peo2-biotinofc_ 191 maleimide-peo2-biotinofc_ -NEM C nemc_ 83 nemc_ -NIPCAM nipcam_ 84 nipcam_ -O18 on peptide n-term o18onpeptiden-term_ 87 o18onpeptiden-term_ -PNGasF in O18 water pngasfino18water_ 139 pngasfino18water_ -SeMet semet_ 113 semet_ -Serine HexNAc serinehexnac_ 184 serinehexnac_ -TMT 6-plex on K tmt6-plexonk_ 198 tmt6-plexonk_ -TMT 6-plex on n-term peptide tmt6-plexonn-termpeptide_ 199 tmt6-plexonn-termpeptide_ -Threonine HexNAc threoninehexnac_ 185 threoninehexnac_ -Uniblue A on K uniblueaonk_ 195 uniblueaonk_ -acetylation of K acetylationofk_ 24 acetylationofk_ -acetylation of protein n-term acetylationofproteinn-term_ 10 acetylationofproteinn-term_ -amidation of peptide c-term amidationofpeptidec-term_ 25 amidationofpeptidec-term_ -arginine to ornithine argininetoornithine_ 163 argininetoornithine_ -beta elimination of S betaeliminationofs_ 140 betaeliminationofs_ -beta elimination of T betaeliminationoft_ 141 betaeliminationoft_ -beta methythiolation of D betamethythiolationofd_ 13 betamethythiolationofd_ -beta-carboxylation of D beta-carboxylationofd_ 47 beta-carboxylationofd_ -beta-methylthiolation of D (duplicate of 13) beta-methylthiolationofd_duplicateof13__ 26 beta-methylthiolationofd_duplicateof13__ -carbamidomethyl C carbamidomethylc_ 3 carbamidomethylc_ -carbamylation of K carbamylationofk_ 31 carbamylationofk_ -carbamylation of n-term peptide carbamylationofn-termpeptide_ 32 carbamylationofn-termpeptide_ -carboxyamidomethylation of D carboxyamidomethylationofd_ 29 carboxyamidomethylationofd_ -carboxyamidomethylation of E carboxyamidomethylationofe_ 30 carboxyamidomethylationofe_ -carboxyamidomethylation of H carboxyamidomethylationofh_ 28 carboxyamidomethylationofh_ -carboxyamidomethylation of K carboxyamidomethylationofk_ 27 carboxyamidomethylationofk_ -carboxykynurenin of W carboxykynureninofw_ 165 carboxykynureninofw_ -carboxymethyl C carboxymethylc_ 2 carboxymethylc_ -carboxymethylated selenocysteine carboxymethylatedselenocysteine_ 207 carboxymethylatedselenocysteine_ -citrullination of R citrullinationofr_ 33 citrullinationofr_ -deamidation of N deamidationofn_ 196 deamidationofn_ -deamidation of N and Q deamidationofnandq_ 4 deamidationofnandq_ -dehydro of S and T dehydroofsandt_ 164 dehydroofsandt_ -di-O18 on peptide n-term di-o18onpeptiden-term_ 88 di-o18onpeptiden-term_ -di-iodination of Y di-iodinationofy_ 35 di-iodinationofy_ -di-methylation of K di-methylationofk_ 36 di-methylationofk_ -di-methylation of R di-methylationofr_ 37 di-methylationofr_ -di-methylation of peptide n-term di-methylationofpeptiden-term_ 38 di-methylationofpeptiden-term_ -farnesylation of C farnesylationofc_ 42 farnesylationofc_ -fluorophenylalanine fluorophenylalanine_ 46 fluorophenylalanine_ -formylation of K formylationofk_ 43 formylationofk_ -formylation of peptide n-term formylationofpeptiden-term_ 44 formylationofpeptiden-term_ -formylation of protein n-term formylationofproteinn-term_ 82 formylationofproteinn-term_ -gamma-carboxylation of E gamma-carboxylationofe_ 48 gamma-carboxylationofe_ -gammathiopropionylation of K gammathiopropionylationofk_ 40 gammathiopropionylationofk_ -gammathiopropionylation of peptide n-term gammathiopropionylationofpeptiden-term_ 41 gammathiopropionylationofpeptiden-term_ -geranyl-geranyl geranyl-geranyl_ 49 geranyl-geranyl_ -glucuronylation of protein n-term glucuronylationofproteinn-term_ 50 glucuronylationofproteinn-term_ -glutathione disulfide glutathionedisulfide_ 51 glutathionedisulfide_ -guanidination of K guanidinationofk_ 53 guanidinationofk_ -heavy arginine-13C6 heavyarginine-13c6_ 136 heavyarginine-13c6_ -heavy arginine-13C6-15N4 heavyarginine-13c6-15n4_ 137 heavyarginine-13c6-15n4_ -heavy lysine - 13C6 15N2 heavylysine-13c615n2_ 181 heavylysine-13c615n2_ -heavy lysine - 2H4 heavylysine-2h4_ 180 heavylysine-2h4_ -heavy lysine-13C6 heavylysine-13c6_ 138 heavylysine-13c6_ -homoserine homoserine_ 56 homoserine_ -homoserine lactone homoserinelactone_ 57 homoserinelactone_ -hydroxylation of Y hydroxylationofy_ 64 hydroxylationofy_ -hydroxylation of D hydroxylationofd_ 59 hydroxylationofd_ -hydroxylation of F hydroxylationoff_ 63 hydroxylationoff_ -hydroxylation of K hydroxylationofk_ 60 hydroxylationofk_ -hydroxylation of N hydroxylationofn_ 61 hydroxylationofn_ -hydroxylation of P hydroxylationofp_ 62 hydroxylationofp_ -iTRAQ114 on K itraq114onk_ 168 itraq114onk_ -iTRAQ114 on Y itraq114ony_ 169 itraq114ony_ -iTRAQ114 on nterm itraq114onnterm_ 167 itraq114onnterm_ -iTRAQ115 on K itraq115onk_ 171 itraq115onk_ -iTRAQ115 on Y itraq115ony_ 172 itraq115ony_ -iTRAQ115 on nterm itraq115onnterm_ 170 itraq115onnterm_ -iTRAQ116 on K itraq116onk_ 174 itraq116onk_ -iTRAQ116 on Y itraq116ony_ 175 itraq116ony_ -iTRAQ116 on nterm itraq116onnterm_ 173 itraq116onnterm_ -iTRAQ117 on K itraq117onk_ 177 itraq117onk_ -iTRAQ117 on Y itraq117ony_ 178 itraq117ony_ -iTRAQ117 on nterm itraq117onnterm_ 176 itraq117onnterm_ -iTRAQ8plex itraq8plex_ 204 itraq8plex_ -iTRAQ8plex itraq8plex_ 205 itraq8plex_ -iTRAQ8plex itraq8plex_ 203 itraq8plex_ -iTRAQ8plex itraq8plex_ 201 itraq8plex_ -iTRAQ8plex itraq8plex_ 202 itraq8plex_ -iTRAQ8plex itraq8plex_ 200 itraq8plex_ -iodination of Y iodinationofy_ 65 iodinationofy_ -lipoyl K lipoylk_ 67 lipoylk_ -methyl C methylc_ 73 methylc_ -methyl H methylh_ 74 methylh_ -methyl N methyln_ 75 methyln_ -methyl R methylr_ 77 methylr_ -methyl ester of D methylesterofd_ 69 methylesterofd_ -methyl ester of E (duplicate of 17) methylesterofe_duplicateof17__ 70 methylesterofe_duplicateof17__ -methyl ester of S methylesterofs_ 71 methylesterofs_ -methyl ester of Y methylesterofy_ 72 methylesterofy_ -methyl ester of peptide c-term (duplicate of 18) methylesterofpeptidec-term_duplicateof18__ 68 methylesterofpeptidec-term_duplicateof18__ -methylation of D methylationofd_ 16 methylationofd_ -methylation of E methylationofe_ 17 methylationofe_ -methylation of K methylationofk_ 0 methylationofk_ -methylation of Q methylationofq_ 14 methylationofq_ -methylation of peptide c-term methylationofpeptidec-term_ 18 methylationofpeptidec-term_ -methylation of peptide n-term methylationofpeptiden-term_ 76 methylationofpeptiden-term_ -methylation of protein n-term methylationofproteinn-term_ 11 methylationofproteinn-term_ -myristoleylation of G myristoleylationofg_ 78 myristoleylationofg_ -myristoyl-4H of G myristoyl-4hofg_ 79 myristoyl-4hofg_ -myristoylation of K myristoylationofk_ 81 myristoylationofk_ -myristoylation of peptide n-term G myristoylationofpeptiden-termg_ 80 myristoylationofpeptiden-termg_ -n-acyl diglyceride cysteine n-acyldiglyceridecysteine_ 118 n-acyldiglyceridecysteine_ -n-formyl met addition n-formylmetaddition_ 22 n-formylmetaddition_ -oxidation of C oxidationofc_ 193 oxidationofc_ -oxidation of C to cysteic acid oxidationofctocysteicacid_ 34 oxidationofctocysteicacid_ -oxidation of C to sulfinic acid oxidationofctosulfinicacid_ 162 oxidationofctosulfinicacid_ -oxidation of F to dihydroxyphenylalanine oxidationofftodihydroxyphenylalanine_ 39 oxidationofftodihydroxyphenylalanine_ -oxidation of H oxidationofh_ 89 oxidationofh_ -oxidation of H to D oxidationofhtod_ 55 oxidationofhtod_ -oxidation of H to N oxidationofhton_ 54 oxidationofhton_ -oxidation of M oxidationofm_ 1 oxidationofm_ -oxidation of P to pyroglutamic acid oxidationofptopyroglutamicacid_ 111 oxidationofptopyroglutamicacid_ -oxidation of W oxidationofw_ 90 oxidationofw_ -oxidation of W to formylkynurenin oxidationofwtoformylkynurenin_ 45 oxidationofwtoformylkynurenin_ -oxidation of W to hydroxykynurenin oxidationofwtohydroxykynurenin_ 58 oxidationofwtohydroxykynurenin_ -oxidation of W to kynurenin oxidationofwtokynurenin_ 66 oxidationofwtokynurenin_ -oxidation of W to nitro oxidationofwtonitro_ 85 oxidationofwtonitro_ -oxidation of Y (duplicate of 64) oxidationofy_duplicateof64__ 194 oxidationofy_duplicateof64__ -oxidation of Y to nitro oxidationofytonitro_ 86 oxidationofytonitro_ -palmitoleyl of C palmitoleylofc_ 187 palmitoleylofc_ -palmitoleyl of S palmitoleylofs_ 186 palmitoleylofs_ -palmitoleyl of T palmitoleyloft_ 188 palmitoleyloft_ -palmitoylation of C palmitoylationofc_ 92 palmitoylationofc_ -palmitoylation of K palmitoylationofk_ 93 palmitoylationofk_ -palmitoylation of S palmitoylationofs_ 94 palmitoylationofs_ -palmitoylation of T palmitoylationoft_ 95 palmitoylationoft_ -phosphopantetheine S phosphopantetheines_ 91 phosphopantetheines_ -phosphorylation of H phosphorylationofh_ 192 phosphorylationofh_ -phosphorylation of S phosphorylationofs_ 6 phosphorylationofs_ -phosphorylation of S with ETD loss phosphorylationofswithetdloss_ 134 phosphorylationofswithetdloss_ -phosphorylation of S with prompt loss phosphorylationofswithpromptloss_ 96 phosphorylationofswithpromptloss_ -phosphorylation of T phosphorylationoft_ 7 phosphorylationoft_ -phosphorylation of T with ETD loss phosphorylationoftwithetdloss_ 135 phosphorylationoftwithetdloss_ -phosphorylation of T with prompt loss phosphorylationoftwithpromptloss_ 97 phosphorylationoftwithpromptloss_ -phosphorylation of Y phosphorylationofy_ 8 phosphorylationofy_ -phosphorylation with neutral loss on C phosphorylationwithneutrallossonc_ 99 phosphorylationwithneutrallossonc_ -phosphorylation with neutral loss on D phosphorylationwithneutrallossond_ 100 phosphorylationwithneutrallossond_ -phosphorylation with neutral loss on H phosphorylationwithneutrallossonh_ 101 phosphorylationwithneutrallossonh_ -phosphorylation with neutral loss on S phosphorylationwithneutrallossons_ 132 phosphorylationwithneutrallossons_ -phosphorylation with neutral loss on T phosphorylationwithneutrallossont_ 133 phosphorylationwithneutrallossont_ -phosphorylation with prompt loss on Y phosphorylationwithpromptlossony_ 98 phosphorylationwithpromptlossony_ -propionamide C propionamidec_ 5 propionamidec_ -propionyl heavy K propionylheavyk_ 104 propionylheavyk_ -propionyl heavy peptide n-term propionylheavypeptiden-term_ 105 propionylheavypeptiden-term_ -propionyl light K propionyllightk_ 102 propionyllightk_ -propionyl light on peptide n-term propionyllightonpeptiden-term_ 103 propionyllightonpeptiden-term_ -pyridyl K pyridylk_ 106 pyridylk_ -pyridyl peptide n-term pyridylpeptiden-term_ 107 pyridylpeptiden-term_ -pyro-cmC pyro-cmc_ 108 pyro-cmc_ -pyro-glu from n-term E pyro-glufromn-terme_ 109 pyro-glufromn-terme_ -pyro-glu from n-term Q pyro-glufromn-termq_ 110 pyro-glufromn-termq_ -s-pyridylethylation of C s-pyridylethylationofc_ 112 s-pyridylethylationofc_ -selenocysteine selenocysteine_ 206 selenocysteine_ -sulfation of Y sulfationofy_ 114 sulfationofy_ -sulphone of M sulphoneofm_ 115 sulphoneofm_ -sumoylation of K sumoylationofk_ 166 sumoylationofk_ -tri-deuteromethylation of D tri-deuteromethylationofd_ 19 tri-deuteromethylationofd_ -tri-deuteromethylation of E tri-deuteromethylationofe_ 20 tri-deuteromethylationofe_ -tri-deuteromethylation of peptide c-term tri-deuteromethylationofpeptidec-term_ 21 tri-deuteromethylationofpeptidec-term_ -tri-iodination of Y tri-iodinationofy_ 116 tri-iodinationofy_ -tri-methylation of K tri-methylationofk_ 15 tri-methylationofk_ -tri-methylation of R tri-methylationofr_ 117 tri-methylationofr_ -tri-methylation of protein n-term tri-methylationofproteinn-term_ 12 tri-methylationofproteinn-term_ -trideuteration of L (SILAC) trideuterationofl_silac__ 197 trideuterationofl_silac__ -ubiquitinylation residue ubiquitinylationresidue_ 52 ubiquitinylationresidue_ diff -r a929e27eb203 -r deaedec14cc8 tool-data/pepxml_databases.loc.sample --- a/tool-data/pepxml_databases.loc.sample Thu Jun 21 22:30:48 2012 -0400 +++ /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 a929e27eb203 -r deaedec14cc8 tool-data/protk_display_site.txt.sample --- a/tool-data/protk_display_site.txt.sample Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -#Proteomic Visualization application should be hosted on the same server as galaxy -#Entries in this file are of the format "site_id" site_url -Proteomics Visualize http://127.0.0.1:8500 diff -r a929e27eb203 -r deaedec14cc8 tool-data/tandem_mods.loc.sample --- a/tool-data/tandem_mods.loc.sample Thu Jun 21 22:30:48 2012 -0400 +++ /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 a929e27eb203 -r deaedec14cc8 xls_to_table.xml --- a/xls_to_table.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ - - protk - Converts an excel spreadsheet to a tab delimited text file - - - -xls_to_table.rb $input_file -o $output - - - - - - - - - - - - - Convert an Excel Spreadsheet to Tab delimited text - - -