Mercurial > repos > iracooke > xtandem
changeset 18:529ea20c1e6c draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
| author | iracooke |
|---|---|
| date | Sun, 24 May 2015 01:12:42 -0400 |
| parents | aadf13041508 |
| children | fc1decb780ba |
| files | README README.md README.rst repository_dependencies.xml tandem.xml tandem_to_pepxml.xml test-data/tandem_to_pepxml_test.tandem test-data/testdb.fasta test-data/tiny.mzML tool_dependencies.xml |
| diffstat | 10 files changed, 1737 insertions(+), 211 deletions(-) [+] |
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--- a/README Mon Jan 05 00:56:19 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -Galaxy wrapper for running the X!Tandem search engine and converting results to pepXML - -Requirements: -This package uses protk and the trans_proteomic_pipeline. These must be installed separately. - -For instructions please see: https://github.com/iracooke/protk/#galaxy-integration \ No newline at end of file
--- a/README.md Mon Jan 05 00:56:19 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -## What is it? -Galaxy tool definition file and wrapper scripts for the [X!Tandem search engine](http://www.thegpm.org/tandem/index.html). - -## This tool requires that the protk rubygem and X!Tandem itself are installed. - -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sun May 24 01:12:42 2015 -0400 @@ -0,0 +1,39 @@ +X!Tandem +======== + +Galaxy wrapper for running the X!Tandem search engine and converting results to pepXML + +Requirements +------------ + +This package uses protk_ and the trans_proteomic_pipeline_ which need to be present in order for the tool to work. + +.. _protk: https://github.com/iracooke/protk +.. _trans_proteomic_pipeline: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP + +There are two ways you can satify these dependencies (choose one): + +1. **Manual Install:** Details on how to install protk_ and the trans_proteomic_pipeline_ manually are available here_. + +2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work. The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed. + +.. _docker: https://www.docker.com/ +.. _here: https://github.com/iracooke/protk/#galaxy-integration +.. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker +__ container_ + + +Further Info +------------ + +The source code for this tool and other protk galaxy tools is on github_. Please visit the github page to contribute to the project or to `report an issue`__ + +.. _github: https://github.com/iracooke/protk-galaxytools +.. _issue: https://github.com/iracooke/protk-galaxytools/issues +__ issue_ + + +Please visit the XTandem_ page on the GPM website for details of the search engine itself. + +.. _XTandem: http://www.thegpm.org/tandem/ +
--- a/repository_dependencies.xml Mon Jan 05 00:56:19 2015 -0500 +++ b/repository_dependencies.xml Sun May 24 01:12:42 2015 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="Proteomics datatypes"> - <repository changeset_revision="9cfabf0b942d" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="6ab4a0bf67df" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>
--- a/tandem.xml Mon Jan 05 00:56:19 2015 -0500 +++ b/tandem.xml Sun May 24 01:12:42 2015 -0400 @@ -1,194 +1,180 @@ -<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.4"> - +<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.0"> + <description>Run an X!Tandem Search</description> <requirements> - <container type="docker">simonalpha/protk:1.4.0</container> - <requirement type="package" version="1.4">protk</requirement> - </requirements> - - <description>Run an X!Tandem Search</description> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4.2">protk</requirement> + </requirements> + <command> + #if $database.source_select=="built_in": + tandem_search.rb -d $database.dbkey + #else + tandem_search.rb -d $database.fasta_file + #end if - <command> - #if $database.source_select=="built_in": - tandem_search.rb -d $database.dbkey - #else - tandem_search.rb -d $database.fasta_file - #end if - - #if $tandem_params.source_select=="built_in": - -T $tandem_params.paramskey - #else - -T $tandem_params.params_file - #end if + #if $tandem_params.source_select=="built_in": + -T $tandem_params.paramskey + #else + -T $tandem_params.params_file + #end if - --var-mods=' - $variable_mods - #for $custom_variable_mod in $custom_variable_mods: - ,${custom_variable_mod.custom_mod} - #end for - ' + --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 + --fix-mods=' + $fixed_mods + #for $custom_fix_mod in $custom_fix_mods: + ,${custom_fix_mod.custom_mod} + #end for + ' - --precursor-ion-tol-units=$precursor_tolu - - -v $missed_cleavages + $input_file -o $output -r - -f $fragment_ion_tol - - -p $precursor_ion_tol - - $allow_multi_isotope_search + --enzyme=$enzyme - $acetyl_protein_nterm - - $cleavage_semi - - $keep_spectra - - --threads $threads - - </command> + --precursor-ion-tol-units=$precursor_tolu + -v $missed_cleavages + -f $fragment_ion_tol + -p $precursor_ion_tol + $allow_multi_isotope_search + $acetyl_protein_nterm + $cleavage_semi + $keep_spectra + --threads "\${GALAXY_SLOTS:-1}" - <inputs> - <conditional name="database"> - <param name="source_select" type="select" label="Database source"> - <option value="built_in">Built-In</option> - <option value="input_ref" selected="true">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> - - <conditional name="tandem_params"> - <param name="source_select" type="select" label="Baseline Parameters"> - <option value="built_in" selected="true">Built-In</option> - <option value="input_ref">Custom parameter file</option> - </param> - <when value="built_in"> - <param name="paramskey" type="select" format="text" > - <label>Paramset</label> - <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option> - <option value="isb_native">ISB Native</option> - <option value="gpm">GPM</option> - </param> - </when> - <when value="input_ref"> - <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" /> - </when> - </conditional> + </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" selected="true">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> + <conditional name="tandem_params"> + <param name="source_select" type="select" label="Baseline Parameters"> + <option value="built_in" selected="true">Built-In</option> + <option value="input_ref">Custom parameter file</option> + </param> + <when value="built_in"> + <param name="paramskey" type="select" format="text" > + <label>Paramset</label> + <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option> + <option value="isb_native">ISB Native</option> + <option value="gpm">GPM</option> + </param> + </when> + <when value="input_ref"> + <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" /> + </when> + </conditional> - <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A file with MS/MS data"/> + <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A 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> - <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_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> - <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="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" /> - + <param name="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" /> + <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 selected="true" value="2">2</option> + </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 selected="true" value="2">2</option> - </param> - - <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/> - - <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/> + <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/> + <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/> - <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/> - - <param name="enzyme" type="select" format="text"> - <label>Enzyme</label> - <option value="[R]__pc__{P}">argc - [R]|{P}</option> - <option value="[X]__pc__[D]">aspn - [X]|[D]</option> - <option value="[FLMWY]__pc__{P}">chymotrypsin - [FLMWY]|{P}</option> - <option value="[R]__pc__[X]">clostripain - [R]|[X]</option> - <option value="[M]__pc__{X}">cnbr - [M]|{X}</option> - <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option> - <option value="[D]__pc__{P}">formicacid - [D]|{P}</option> - <option value="[DE]__pc__{P}">gluc - [DE]|{P}</option> - <option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option> - <option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option> - <option value="[K]__pc__{P}">lysc - [K]|{P}</option> - <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option> - <option value="[X]__pc__[K]">lysn - [X]|[K]</option> - <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option> - <option value="[X]__pc__[X]">nonspecific - [X]|[X]</option> - <option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option> - <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option> - <option value="[E]__pc__[X]">staph_protease - [E]|[X]</option> - <option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option> - <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option> - <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option> - <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option> - <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option> - </param> + <param name="enzyme" type="select" format="text"> + <label>Enzyme</label> + <option value="[R]__pc__{P}">argc - [R]|{P}</option> + <option value="[X]__pc__[D]">aspn - [X]|[D]</option> + <option value="[FLMWY]__pc__{P}">chymotrypsin - [FLMWY]|{P}</option> + <option value="[R]__pc__[X]">clostripain - [R]|[X]</option> + <option value="[M]__pc__{X}">cnbr - [M]|{X}</option> + <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option> + <option value="[D]__pc__{P}">formicacid - [D]|{P}</option> + <option value="[DE]__pc__{P}">gluc - [DE]|{P}</option> + <option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option> + <option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option> + <option value="[K]__pc__{P}">lysc - [K]|{P}</option> + <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option> + <option value="[X]__pc__[K]">lysn - [X]|[K]</option> + <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option> + <option value="[X]__pc__[X]">nonspecific - [X]|[X]</option> + <option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option> + <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option> + <option value="[E]__pc__[X]">staph_protease - [E]|[X]</option> + <option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option> + <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option> + <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option> + <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option> + <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option> + </param> - - <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/> - - <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" 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="--multi-isotope-search" falsevalue=""/> - - </inputs> - - - <outputs> - <data format="tandem" 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}.${input_file.display_name}.tandem"/> - </outputs> - - + <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/> + <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/> + <param name="precursor_tolu" type="select" format="text"> + <label>Precursor Ion Tolerance Units</label> + <option value="ppm">ppm</option> + <option value="Da">Da</option> + </param> + <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/> + </inputs> + <outputs> + <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/> + </outputs> + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="source_select" value="input_ref"/> + <param name="fasta_file" value="testdb.fasta" format="fasta"/> + <param name="input_file" value="tiny.mzML" format="mzml"/> + <output name="output" format="tandem"> + <assert_contents> + <has_text text="tandem-style" /> + </assert_contents> + </output> + </test> + </tests> <help> **What it does**
--- a/tandem_to_pepxml.xml Mon Jan 05 00:56:19 2015 -0500 +++ b/tandem_to_pepxml.xml Sun May 24 01:12:42 2015 -0400 @@ -1,26 +1,33 @@ -<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.0.2"> - <requirements> - <container type="docker">simonalpha/protk:1.4.0</container> - <requirement type="package" version="1.4">protk</requirement> - <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> - </requirements> +<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.0"> + <description>Converts a tandem result file to pepXML</description> + <requirements> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4.2">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> + </requirements> + <command> + tandem_to_pepxml.rb $input_file -o $output + </command> - <description>Converts a tandem result file to pepXML</description> - -<command> - tandem_to_pepxml.rb $input_file -o $output -</command> + <inputs> + <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/> + </inputs> -<inputs> - <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/> -</inputs> - -<outputs> - <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" /> -</outputs> - -<help> - Convert X!Tandem results to pepXML -</help> - + <outputs> + <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" /> + </outputs> + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="input_file" value="tandem_to_pepxml_test.tandem" format="tandem"/> + <output name="output" format="raw_pepxml"> + <assert_contents> + <has_text text="SQVFQLESTFDV" /> + </assert_contents> + </output> + </test> + </tests> + <help> + Convert X!Tandem results to pepXML + </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tandem_to_pepxml_test.tandem Sun May 24 01:12:42 2015 -0400 @@ -0,0 +1,1145 @@ +<?xml version="1.0"?> +<?xml-stylesheet type="text/xsl" href="tandem-style.xsl"?> +<bioml xmlns:GAML="http://www.bioml.com/gaml/" label="models from '/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8167.d.mgf'"> +<group id="1" mh="1443.700944" z="2" rt="" expect="5.9e-02" label="tr|O16132|O16132_HYDVU NK-2 class homeobox transcription factor OS=Hydra vulgaris..." type="model" sumI="3.89" maxI="899" fI="8.99" act="0" > +<protein expect="-1.2" id="1.1" uid="14" label="tr|O16132|O16132_HYDVU NK-2 class homeobox transcription factor OS=Hydra vulgaris..." sumI="4.77" > +<note label="description">tr|O16132|O16132_HYDVU NK-2 class homeobox transcription factor OS=Hydra vulgaris GN=CnNK-2 PE=2 SV=1</note> +<file type="peptide" URL="/Users/icooke/Desktop/iptest/AASequences.fasta"/> +<peptide start="1" end="328"> + +<domain id="1.1.1" start="257" end="269" expect="5.9e-02" mh="1379.728" delta="63.973" hyperscore="24.9" nextscore="22.2" y_score="13.5" y_ions="6" b_score="0.0" b_ions="0" pre="FQHR" post="DVCL" seq="NVPVLVQNNQVSS" missed_cleavages="0"> +</domain> +</peptide> +</protein> +</group> +<group id="2" mh="1249.669838" z="3" rt="" expect="1.9e+00" label="sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2..." type="model" sumI="3.67" maxI="388" fI="3.88" act="0" > +<protein expect="0.0" id="2.1" uid="19" label="sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2..." sumI="5.26" > +<note label="description">sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1</note> +<file type="peptide" URL="/Users/icooke/Desktop/iptest/AASequences.fasta"/> +<peptide start="1" end="741"> + +<domain id="2.1.1" start="87" end="96" expect="1.9e+00" mh="1210.479" delta="39.191" hyperscore="21.6" nextscore="20.0" y_score="8.8" y_ions="4" b_score="9.8" 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