Mercurial > repos > iracooke > protk
changeset 1:deaedec14cc8 draft
Improved help text to include proper citations
| author | iracooke |
|---|---|
| date | Mon, 23 Jul 2012 00:16:43 -0400 |
| parents | a929e27eb203 |
| children | 418f42b34049 |
| files | display_applications/proteomics/PepXml.xml display_applications/proteomics/ProtXml.xml display_applications/proteomics/mzML.xml interprophet.xml interprophet_wrapper.rb lib/galaxy/datatypes/proteomics.py make_decoy.xml mzml_to_mgf.xml omssa.xml peptide_prophet.xml peptide_prophet_wrapper.rb pepxml_to_table.xml protein_prophet.xml protein_prophet_wrapper.rb tandem.xml tool-data/datatypes_conf.xml tool-data/mascot_databases.loc.sample tool-data/mascot_mods.loc.sample tool-data/omssa_mods.loc.sample tool-data/pepxml_databases.loc.sample tool-data/protk_display_site.txt.sample tool-data/tandem_mods.loc.sample xls_to_table.xml |
| diffstat | 23 files changed, 0 insertions(+), 1225 deletions(-) [+] |
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--- 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 @@ -<display id="proteomics_pepxml" version="1.0.0" name="view pepXML in"> - <dynamic_links from_file="tool-data/protk_display_site.txt" skip_startswith="#" id="0" name="0"> - <!-- Define parameters by column from file --> - <dynamic_param name="site_id" value="0"/> - <dynamic_param name="site_url" value="1"/> - <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> - <url target_frame="galaxy_main">${site_url}/init_local?file=${encoded_filename.qp}&type=pepxml</url> - <param type="data" name="pep_file" viewable="False" format="pepXML"/> - <param type="data" dataset="pep_file" name="pepxml_file" format="pepXML" viewable="False" /> - <param type="template" name="encoded_filename" strip="True" > - #import binascii - ${binascii.hexlify( $pepxml_file.file_name )} - </param> - <param type="template" name="galaxy_url" strip="True" > - ${BASE_URL.split(":")[1][2:]} - </param> - </dynamic_links> -</display>
--- a/display_applications/proteomics/ProtXml.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -<display id="proteomics_protxml" version="1.0.0" name="view protXML in"> - <dynamic_links from_file="tool-data/protk_display_site.txt" skip_startswith="#" id="0" name="0"> - <!-- Define parameters by column from file --> - <dynamic_param name="site_id" value="0"/> - <dynamic_param name="site_url" value="1"/> - <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> - <url target_frame="galaxy_main">${site_url}/init_local?file=${encoded_filename.qp}&type=protxml</url> - <param type="data" name="prot_file" viewable="False" format="protXML"/> - <param type="data" dataset="prot_file" name="protxml_file" format="protXML" viewable="False" /> - <param type="template" name="encoded_filename" strip="True" > - #import binascii - ${binascii.hexlify( $protxml_file.file_name )} - </param> - <param type="template" name="galaxy_url" strip="True" > - ${BASE_URL.split(":")[1][2:]} - </param> - </dynamic_links> -</display> \ No newline at end of file
--- a/display_applications/proteomics/mzML.xml Thu Jun 21 22:30:48 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -<display id="proteomics_mzml" version="1.0.2" name="view mzML data"> - <dynamic_links from_file="tool-data/protk_display_site.txt" skip_startswith="#" id="0" name="0"> - <!-- Define parameters by column from file --> - <dynamic_param name="site_id" value="0"/> - <dynamic_param name="site_url" value="1"/> - <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> - <url target_frame="galaxy_main">${site_url}/init_local?file=${encoded_filename.qp}&type=mzml</url> - <param type="data" name="raw_file" viewable="False" format="mzML"/> - <param type="data" dataset="raw_file" name="mzml_file" format="mzML" viewable="False" /> - <param type="template" name="encoded_filename" strip="True" > - #import binascii - ${binascii.hexlify( $mzml_file.file_name )} - </param> - <param type="template" name="galaxy_url" strip="True" > - ${BASE_URL.split(":")[1][2:]} - </param> - </dynamic_links> -</display> \ No newline at end of file
--- 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 @@ -<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.0"> - <requirements><requirement type="package">protk</requirement></requirements> - <description>Combine Peptide Prophet results from multiple search engines</description> - - <command interpreter="ruby"> - - 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: - ${input_file.additional_input} - #end for - - </command> - - <inputs> - - <param name="first_input" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> - - <repeat name="input_files" title="Additional PepXML Input Files"> - <param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/> - </repeat> - - <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--nonss"/> - <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--nonrs"/> - <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--nonse"/> - <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--nonsi"/> - <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--nonsm"/> - - <param name="minprob" type="text" label="Minimum threshod probability for reporting results"/> - - </inputs> - <outputs> - <data format="interprophet_pepxml" name="output" metadata_source="first_input" label="interprophet.${first_input.display_name}" from_work_dir="interprophet_output.pep.xml"/> - </outputs> - - <help> - Run InterProphet - </help> - -</tool>
--- 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}] -
--- 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("^<mzML") - for i in range(3): - line = handle.readline() - if xmlns_re.match(line.strip()): - handle.close() - return True - - handle.close() - return False - - -class ProtXML( Text ): - """protXML data""" - file_ext = "protxml" - - 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 = 'prot XML Search Results' - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def sniff( self, filename ): - protxml_header = [ '<?xml version="1.0" encoding="ISO-8859-1"?>', - '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 = [ '<?xml version="1.0" encoding="ISO-8859-1"?>', - '<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_2.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_2.1 http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/mzXML_idx_2.1.xsd">' ] - 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
--- 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 @@ -<tool id="make_decoy_1" name="Create decoy databases" version="1.0.0"> - <requirements> - <requirement type="package">protk</requirement> - </requirements> - - <description>Creates a random protein database with similar properties to a real protein database</description> - - <command>make_decoy.rb $input_file -o $output -L $length -P $prefix $append</command> - - <inputs> - - <param name="input_file" type="data" format="fasta" multiple="false" label="Input File" help="Real protein sequences. Take care that these are fasta formatted with no more than 80 amino acids per line. There should be no whitespace in the sequences."/> - <param name="prefix" type="text" label="String to prepend to generated protein ID's" size="60" value="decoy_"/> - <param name="length" type="text" label="Number of random sequences to generate" help="If 0, a database of equal size to the input database will be generated" size="60" value="0"/> - <param name="append" type="boolean" checked="true" label="Append input dataset to the generated sequences" truevalue="-A" falsevalue=""/> - </inputs> - - <outputs> - <data format="fasta" name="output" metadata_source="input_file" label="Random sequences from ${input_file.display_name}" from_work_dir="random.fasta"/> - </outputs> - - <help> - Create random protein sequences - </help> - -</tool>
--- 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 @@ -<tool id="mzml_to_mgf_1" name="MzML to mgf" version="1.0.0"> - <requirements> - <requirement type="package">protk</requirement> - </requirements> - - <description>Converts an mzML file to mgf suitable for searching by omssa</description> - - <command>file_convert.rb $input_file -o $output $maldi</command> - - <inputs> - - <param name="input_file" type="data" format="mzml" multiple="false" label="Input File" help="Line Spectra in mzML format"/> - <param name="maldi" type="boolean" label="Is the data from a MALDI instrument" truevalue="-l" falsevalue=""/> - - </inputs> - - <outputs> - <data format="mgf" name="output" metadata_source="input_file" label="${input_file.display_name}.mgf" from_work_dir="converted.mgf"/> - </outputs> - - <help> - Convert line spectra to Mascot Generic Format - </help> - -</tool>
--- 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 @@ -<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.0"> - <requirements> - <requirement type="package">protk</requirement> - </requirements> - - <description>Run an OMSSA MS/MS Search</description> - - <command>#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 - - </command> - - - <inputs> - <conditional name="database"> - <param name="source_select" type="select" label="Database source"> - <option value="built_in">Built-In</option> - <option value="input_ref">Uploaded fasta file</option> - </param> - <when value="built_in"> - <param name="dbkey" type="select" format="text" > - <label>Database</label> - <options from_file="pepxml_databases.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - </when> - <when value="input_ref"> - <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> - </when> - </conditional> - - <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="An mgf file with MS/MS data"/> - - <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while - clicking to select multiple items"> - <options from_file="omssa_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - - <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while - clicking to select multiple items"> - <options from_file="omssa_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - - - <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites"> - <label>Missed Cleavages Allowed</label> - <option value="0">0</option> - <option value="1">1</option> - <option value="2">2</option> - </param> - - <param name="enzyme" type="select" format="text"> - <label>Enzyme</label> - <option value="0">Trypsin</option> - <option value="1">Arg-C</option> - <option value="2">CNBr</option> - <option value="3">Chymotrypsin (FYWL)</option> - <option value="4">Formic Acid</option> - <option value="5">Lys-C</option> - <option value="6">Lys-C, no P rule</option> - <option value="7">Pepsin A</option> - <option value="8">Trypsin+CNBr</option> - <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option> - <option value="10">Trypsin, no P rule</option> - <option value="11">Whole protein</option> - <option value="12">Asp-N</option> - <option value="13">Glu-C</option> - <option value="14">Asp-N+Glu-C</option> - <option value="15">Top-Down</option> - <option value="16">Semi-Tryptic</option> - <option value="17">No Enzyme</option> - <option value="18">Chymotrypsin, no P rule (FYWL)</option> - <option value="19">Asp-N (DE)</option> - <option value="20">Glu-C (DE)</option> - <option value="21">Lys-N (K)</option> - <option value="22">Thermolysin, no P rule</option> - <option value="23">Semi-Chymotrypsin (FYWL)</option> - <option value="24">Semi-Glu-C</option> - </param> - - <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/> - <param name="max_hit_expect" help="Expect values less than this are considered to be hits. Use a large value, eg 10000 when results will be processed downstream with Peptide Prophet" type="float" value="1.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he--> - <param name="intensity_cut_off" help="Peak intensity cut-off as a fraction of maximum peak intensity" type="float" value="0.0005" min="0" max="1" label="Peak intensity cut-off"/><!-- -ci--> - - - <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/> - <param name="precursor_tolu" type="select" format="text"> - <label>Precursor Ion Tolerance Units</label> - <option value="ppm">ppm</option> - <option value="Da">Da</option> - </param> - - <param name="use_average_mass" type="boolean" label="Use average precursor masses" help="Match precursor to average mass of the parent ion instead of its monoisotopic mass" truevalue="-a average" falsevalue=""/> - <param name="respect_precursor_charges" type="boolean" label="Respect precursor charges" help="Use precursor charge information in input file rather than OMSSA's inferred value" truevalue="--respect-charges" falsevalue=""/> - - <param name="multi_isotope" type="select" format="text" help="Include this many neighbouring peaks when searching for a match to the precursor mass. Only used when doing monoisotopic search"> - <label>Multi-isotope search.</label> - <option value="0">0</option> - <option value="1">1</option> - <option value="2">2</option> - <option value="3">3</option> - <option value="4">4</option> - </param> - - <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help=""> - <option selected="true" value="0">a</option> - <option selected="true" value="1">b</option> - <option value="2">c</option> - <option selected="true" value="3">x</option> - <option selected="true" value="4">y</option> - <option value="5">zdot</option> - <option value="10">adot</option> - <option value="11">x-CO2</option> - <option value="12">adot-CO2</option> - </param> - - </inputs> - - <outputs> - <data format="raw_pepxml" name="output" metadata_source="input_file" label="omssa_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.pepXML"/> - </outputs> - - <help> - Run an OMSSA Search - </help> -</tool>
--- 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 @@ -<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.0"> - <requirements><requirement type="package">protk</requirement></requirements> - <description>Calculate Peptide Prophet statistics on search results</description> - - <command interpreter="ruby">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 - </command> - - <inputs> - - <param name="input_file" type="data" format="raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/> - - <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/> - <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue="--no-useicat"/> - <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/> - <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/> - <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/> - <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/> - <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/> - <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/> - <param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/> - <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. - Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/> - <param name="force_fit" type="boolean" label="Force fitting" help="Bypasses automatic mixture model checks and forces fitting of a mixture model" truevalue="--force-fit" falsevalue=""/> - <param name="allow_alt_instruments" type="boolean" label="Allow multiple instrument types" help="Warning instead of exit with error if instrument types between runs is different" truevalue="--allow-alt-instruments" falsevalue=""/> - <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/> - - - </inputs> - <outputs> - <data format="peptideprophet_pepxml" name="output" metadata_source="input_file" label="peptide_prophet.${input_file.display_name}.pep.xml" from_work_dir="peptide_prophet_output.pep.xml"/> - </outputs> - - <help> - Run Peptide Prophet - </help> - - -<!--PeptideProphet options [following the 'O']: - i [use icat information in PeptideProphet] - f [do not use icat information in PeptideProphet] - g [use N-glyc motif information in PeptideProphet] - H [use Phospho information in PeptideProphet] - m [maldi data] - I [use pI information in PeptideProphet] - R [use Hydrophobicity / RT information in PeptideProphet] - F [force the fitting of the mixture model, bypass automatic mixture model checks] - A [use accurate mass binning in PeptideProphet] - w [warning instead of exit with error if instrument types between runs is different] - x [exclude all entries with asterisked score values in PeptideProphet] - l [leave alone all entries with asterisked score values in PeptideProphet] - n [use hardcoded default initialization parameters of the distributions] - P [use Non-parametric model, can only be used with decoy option] - N [do not use the NTT model] - M [do not use the NMC model] - G [use Gamma Distribution to model the Negatives (applies only to X!Tandem data)] - E [only use Expect Score as the Discriminant(applies only to X!Tandem data, - helpful for data with homologous top hits e.g. phospho or glyco)] - d [report decoy hits with a computed probability based on the model learned] - p [run ProteinProphet afterwards] - t [do not create png data plot] - u [do not assemble protein groups in ProteinProphet analysis] - s [do not use Occam's Razor in ProteinProphet analysis to - derive the simplest protein list to explain observed peptides] ---> - -</tool>
--- 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}]
--- 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 @@ -<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.0.0"> - <requirements><requirement type="package">protk</requirement></requirements> - <description>Converts a pepXML file to a tab delimited text file</description> - - -<!-- Note .. the input file is assumed to be the first argument --> -<command>pepxml_to_table.rb $input_file -o $output</command> - - -<inputs> - - <param name="input_file" type="data" format="pepxml" multiple="false" label="Input File" help="A pepXML file"/> - -</inputs> -<outputs> - <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" /> -</outputs> - -<help> - Convert a pepXML file to Tab delimited text -</help> - -</tool>
--- 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 @@ -<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.0"> - <requirements><requirement type="package">protk</requirement></requirements> - <description>Calculate Protein Prophet statistics on search results</description> - - -<!-- Note .. the input file is assumed to be the first argument --> - <command interpreter="ruby">protein_prophet_wrapper.rb $output $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command> - <inputs> - - <param name="input_file" type="data" format="pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/> - - - <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/> - <param name="nooccam" type="boolean" label="Don't apply Occam's razor" help="When selected no attempt will be made to derive the simplest protein list explaining observed peptides" truevalue="--no-occam" falsevalue=""/> - <param name="groupwts" type="boolean" label="Use group weights" help="Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" truevalue="--group-wts" falsevalue=""/> - <param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/> - <param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/> - <param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/> - <param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/> - <param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/> - <param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/> - <param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/> - - <param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/> - <param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/> - - </inputs> - <outputs> - <data format="protxml" name="output" metadata_source="input_file" label="protein_prophet.${input_file.display_name}.protXML" from_work_dir="protein_prophet_results.prot.xml"/> - </outputs> - - -<!--NOPLOT: do not generate plot png file - NOOCCAM: non-conservative maximum protein list - GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check peptide's actual weight against threshold) - NORMPROTLEN: Normalize NSP using Protein Length - LOGPROBS: Use the log of the probabilities in the Confidence calculations - CONFEM: Use the EM to compute probability given the confidence - ALLPEPS: Consider all possible peptides in the database in the confidence model - UNMAPPED: Report results for UNMAPPED proteins - INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment - DELUDE: do NOT use peptide degeneracy information when assessing proteins - - MINPROB: peptideProphet probabilty threshold (default=0.05) - MININDEP: minimum percentage of independent peptides required for a protein (default=0) - - ---> - - <help> - Run Peptide Prophet - </help> - -</tool>
--- 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}] -
--- 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 @@ -<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.0"> - <requirements><requirement type="package">protk</requirement></requirements> - <description>Run an X!Tandem Search</description> - - <command> - #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 - - - - </command> - - <inputs> - <conditional name="database"> - <param name="source_select" type="select" label="Database source"> - <option value="built_in">Built-In</option> - <option value="input_ref">Your Upload File</option> - </param> - <when value="built_in"> - <param name="dbkey" type="select" format="text" > - <label>Database</label> - <options from_file="pepxml_databases.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - </when> - <when value="input_ref"> - <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> - </when> - </conditional> - - <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/> - - - <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while - clicking to select multiple items"> - <options from_file="tandem_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - - <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite)."> - <param name="custom_mod" type="text"> - </param> - </repeat> - - - <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while - clicking to select multiple items"> - <options from_file="tandem_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - - <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite)."> - <param name="custom_mod" type="text"> - </param> - </repeat> - - - - <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites"> - <label>Missed Cleavages Allowed</label> - <option value="0">0</option> - <option value="1">1</option> - <option value="2">2</option> - </param> - - <param name="enzyme" type="select" format="text"> - <label>Enzyme</label> - <option value="Trypsin">Trypsin</option> - </param> - - <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/> - - <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/> - <param name="precursor_tolu" type="select" format="text"> - <label>Precursor Ion Tolerance Units</label> - <option value="ppm">ppm</option> - <option value="Da">Da</option> - </param> - - <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="" falsevalue="--strict-monoisotopic-mass"/> - - </inputs> - - - <outputs> - <data format="raw_pepxml" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/> - </outputs> - - - <help> - Run an X!Tandem Search - </help> - -</tool>
--- 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 @@ -<?xml version="1.0"?> -<datatypes> - <datatype_files> - <datatype_file name="proteomics.py"/> - </datatype_files> - <registration display_path="display_applications"> - <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" display_in_upload="true"> - <display file="proteomics/PepXml.xml" /> - </datatype> - <datatype extension="raw_pepxml" type="galaxy.datatypes.proteomics:PepXml" subclass="true"> - <display file="proteomics/PepXml.xml" /> - </datatype> - <datatype extension="peptideprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" subclass="true"> - <display file="proteomics/PepXml.xml" /> - </datatype> - <datatype extension="interprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" subclass="true"> - <display file="proteomics/PepXml.xml" /> - </datatype> - <datatype extension="protxml" type="galaxy.datatypes.proteomics:ProtXML" display_in_upload="true" > - <display file="proteomics/ProtXml.xml"/> - </datatype> - <datatype extension="mascotdat" type="galaxy.datatypes.proteomics:MascotDat" display_in_upload="false" /> - <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml" display_in_upload="true"> - <display file="proteomics/mzML.xml"/> - </datatype> - <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf" display_in_upload="true" /> - <datatype extension="xls" type="galaxy.datatypes.proteomics:Xls" display_in_upload="true" /> - </registration> - <sniffers> - <sniffer type="galaxy.datatypes.proteomics:MzML"/> - <sniffer type="galaxy.datatypes.proteomics:PepXml"/> - <sniffer type="galaxy.datatypes.proteomics:Mgf"/> - <sniffer type="galaxy.datatypes.proteomics:ProtXML"/> - <sniffer type="galaxy.datatypes.proteomics:MzXML"/> - <sniffer type="galaxy.datatypes.proteomics:Xls"/> - </sniffers> -</datatypes>
--- 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
--- 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_
--- 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_
--- 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_
--- 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
--- 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
--- 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 @@ -<tool id="xls_to_table_1" name="Excel to Table" version="1.0.0"> - <requirements><requirement type="package">protk</requirement></requirements> - <description>Converts an excel spreadsheet to a tab delimited text file</description> - - -<!-- Note .. the input file is assumed to be the first argument --> -<command>xls_to_table.rb $input_file -o $output</command> - - -<inputs> - - <param name="input_file" type="data" format="xls" multiple="false" label="Input File" help="An Excel Spreadsheet"/> - -</inputs> -<outputs> - <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" /> -</outputs> - -<help> - Convert an Excel Spreadsheet to Tab delimited text -</help> - -</tool>