# HG changeset patch
# User iracooke
# Date 1340332248 14400
# Node ID a929e27eb20395d454f80882b783a6296408d2ce
Uploaded
diff -r 000000000000 -r a929e27eb203 display_applications/proteomics/PepXml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/display_applications/proteomics/PepXml.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,18 @@
+
+
+
+
+
+
+ ${site_url}/init_local?file=${encoded_filename.qp}&type=pepxml
+
+
+
+ #import binascii
+ ${binascii.hexlify( $pepxml_file.file_name )}
+
+
+ ${BASE_URL.split(":")[1][2:]}
+
+
+
diff -r 000000000000 -r a929e27eb203 display_applications/proteomics/ProtXml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/display_applications/proteomics/ProtXml.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,18 @@
+
+
+
+
+
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+ ${site_url}/init_local?file=${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 000000000000 -r a929e27eb203 display_applications/proteomics/mzML.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/display_applications/proteomics/mzML.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,18 @@
+
+
+
+
+
+
+ ${site_url}/init_local?file=${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 000000000000 -r a929e27eb203 interprophet.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/interprophet.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,43 @@
+
+ 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:
+ ${input_file.additional_input}
+ #end for
+
+
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+
+ Run InterProphet
+
+
+
diff -r 000000000000 -r a929e27eb203 interprophet_wrapper.rb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/interprophet_wrapper.rb Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,57 @@
+require 'pathname'
+
+$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 000000000000 -r a929e27eb203 lib/galaxy/datatypes/proteomics.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/proteomics.py Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,181 @@
+"""
+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 000000000000 -r a929e27eb203 make_decoy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/make_decoy.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,26 @@
+
+
+ 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
+
+
+
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+
+ Create random protein sequences
+
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+
diff -r 000000000000 -r a929e27eb203 mzml_to_mgf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mzml_to_mgf.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,25 @@
+
+
+ protk
+
+
+ Converts an mzML file to mgf suitable for searching by omssa
+
+ file_convert.rb $input_file -o $output $maldi
+
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+ Convert line spectra to Mascot Generic Format
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diff -r 000000000000 -r a929e27eb203 omssa.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/omssa.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,150 @@
+
+
+ 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
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+ Run an OMSSA Search
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diff -r 000000000000 -r a929e27eb203 peptide_prophet.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/peptide_prophet.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,66 @@
+
+ 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 $maldi
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+ Run Peptide Prophet
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diff -r 000000000000 -r a929e27eb203 peptide_prophet_wrapper.rb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/peptide_prophet_wrapper.rb Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,38 @@
+require 'pathname'
+
+$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 000000000000 -r a929e27eb203 pepxml_to_table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pepxml_to_table.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,23 @@
+
+ protk
+ Converts a pepXML file to a tab delimited text file
+
+
+
+pepxml_to_table.rb $input_file -o $output
+
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+ Convert a pepXML file to Tab delimited text
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diff -r 000000000000 -r a929e27eb203 protein_prophet.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_prophet.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,54 @@
+
+ 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=$minindep
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+ Run Peptide Prophet
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diff -r 000000000000 -r a929e27eb203 protein_prophet_wrapper.rb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_prophet_wrapper.rb Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,37 @@
+require 'pathname'
+
+$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 000000000000 -r a929e27eb203 tandem.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tandem.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,118 @@
+
+ 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
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+ Run an X!Tandem Search
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diff -r 000000000000 -r a929e27eb203 tool-data/datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/datatypes_conf.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,37 @@
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diff -r 000000000000 -r a929e27eb203 tool-data/mascot_databases.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mascot_databases.loc.sample Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,13 @@
+#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 000000000000 -r a929e27eb203 tool-data/mascot_mods.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mascot_mods.loc.sample Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,77 @@
+#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 000000000000 -r a929e27eb203 tool-data/omssa_mods.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/omssa_mods.loc.sample Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,181 @@
+#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 000000000000 -r a929e27eb203 tool-data/pepxml_databases.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/pepxml_databases.loc.sample Thu Jun 21 22:30:48 2012 -0400
@@ -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 000000000000 -r a929e27eb203 tool-data/protk_display_site.txt.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/protk_display_site.txt.sample Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,3 @@
+#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 000000000000 -r a929e27eb203 tool-data/tandem_mods.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tandem_mods.loc.sample Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,6 @@
+#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 000000000000 -r a929e27eb203 xls_to_table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xls_to_table.xml Thu Jun 21 22:30:48 2012 -0400
@@ -0,0 +1,23 @@
+
+ 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
+
+
+