| Previous changeset 13:c60d1f18fd85 (2014-07-01) Next changeset 15:0faaab4f192a (2015-10-20) |
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Commit message:
Docker support and update for protk 1.4 |
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modified:
repository_dependencies.xml tandem.xml tandem_to_pepxml.xml tool-data/tandem_mods.loc.sample |
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added:
README.rst test-data/tandem_to_pepxml_test.tandem test-data/testdb.fasta test-data/tiny.mzML |
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removed:
README |
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| diff -r c60d1f18fd85 -r 9d6e0ad4d600 README --- a/README Tue Jul 01 11:06:33 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r c60d1f18fd85 -r 9d6e0ad4d600 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Mar 26 19:53:53 2015 -0400 |
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| @@ -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/ + |
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| diff -r c60d1f18fd85 -r 9d6e0ad4d600 repository_dependencies.xml --- a/repository_dependencies.xml Tue Jul 01 11:06:33 2014 -0400 +++ b/repository_dependencies.xml Thu Mar 26 19:53:53 2015 -0400 |
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| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="Proteomics datatypes"> - <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ac51d9dbfb4d" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |
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| diff -r c60d1f18fd85 -r 9d6e0ad4d600 tandem.xml --- a/tandem.xml Tue Jul 01 11:06:33 2014 -0400 +++ b/tandem.xml Thu Mar 26 19:53:53 2015 -0400 |
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| @@ -1,7 +1,8 @@ -<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.2"> +<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.0"> <requirements> - <requirement type="package" version="1.3.0">protk</requirement> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4">protk</requirement> </requirements> <description>Run an X!Tandem Search</description> @@ -44,7 +45,7 @@ -f $fragment_ion_tol - -p $precursor_ion_tol + -p $precursor_ion_tol $allow_multi_isotope_search @@ -86,9 +87,9 @@ <when value="built_in"> <param name="paramskey" type="select" format="text" > <label>Paramset</label> - <option value="gpm">GPM</option> + <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option> <option value="isb_native">ISB Native</option> - <option value="isb_kscore">ISB K-Score</option> + <option value="gpm">GPM</option> </param> </when> <when value="input_ref"> @@ -132,7 +133,7 @@ <label>Missed Cleavages Allowed</label> <option value="0">0</option> <option value="1">1</option> - <option value="2">2</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=""/> @@ -143,42 +144,42 @@ <param name="enzyme" type="select" format="text"> <label>Enzyme</label> - <option value="[R]|{P}">argc - [R]|{P}</option> - <option value="[X]|[D]">aspn - [X]|[D]</option> - <option value="[FLMWY]|{P}">chymotrypsin - [FLMWY]|{P}</option> - <option value="[R]|[X]">clostripain - [R]|[X]</option> - <option value="[M]|{P}">cnbr - [M]|{P}</option> - <option value="[AGILV]|{P}">elastase - [AGILV]|{P}</option> - <option value="[D]|{P}">formicacid - [D]|{P}</option> - <option value="[DE]|{P}">gluc - [DE]|{P}</option> - <option value="[E]|{P}">gluc_bicarb - [E]|{P}</option> - <option value="[W]|[X]">iodosobenzoate - [W]|[X]</option> - <option value="[K]|{P}">lysc - [K]|{P}</option> - <option value="[K]|[X]">lysc-p - [K]|[X]</option> - <option value="[X]|[K]">lysn - [X]|[K]</option> - <option value="[X]|[AKRS]">lysn_promisc - [X]|[AKRS]</option> - <option value="[X]|[X]">nonspecific - [X]|[X]</option> - <option value="[FL]|[X]">pepsina - [FL]|[X]</option> - <option value="[P]|[X]">protein_endopeptidase - [P]|[X]</option> - <option value="[E]|[X]">staph_protease - [E]|[X]</option> - <option value="[FMWY]|{P},[KR]|{P},[X]|[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option> - <option value="[KR]|{P}" selected="true">trypsin - [KR]|{P}</option> - <option value="[FKLMRWY]|{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option> - <option value="[KR]|{P},[M]|{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option> - <option value="[DEKR]|{P}">trypsin_gluc - [DEKR]|{P}</option> + <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="0.65" min="0" max="10000" label="Fragment ion tolerance"/> + <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="100" min="0" max="10000" label="Precursor 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="" falsevalue=""/> + <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> @@ -187,7 +188,19 @@ <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** |
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| diff -r c60d1f18fd85 -r 9d6e0ad4d600 tandem_to_pepxml.xml --- a/tandem_to_pepxml.xml Tue Jul 01 11:06:33 2014 -0400 +++ b/tandem_to_pepxml.xml Thu Mar 26 19:53:53 2015 -0400 |
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| @@ -1,25 +1,38 @@ -<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.0.1"> +<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.0"> <requirements> - <requirement type="package" version="1.3.0">protk</requirement> - <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> - </requirements> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> + </requirements> - <description>Converts a tandem result file to pepXML</description> + <description>Converts a tandem result file to pepXML</description> -<command> - tandem_to_pepxml.rb $input_file -o $output -</command> + <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> - -<help> - Convert X!Tandem results to pepXML -</help> + <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> </tool> |
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| diff -r c60d1f18fd85 -r 9d6e0ad4d600 test-data/tandem_to_pepxml_test.tandem --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tandem_to_pepxml_test.tandem Thu Mar 26 19:53:53 2015 -0400 |
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| b'@@ -0,0 +1,1145 @@\n+<?xml version="1.0"?>\n+<?xml-stylesheet type="text/xsl" href="tandem-style.xsl"?>\n+<bioml xmlns:GAML="http://www.bioml.com/gaml/" label="models from \'/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8167.d.mgf\'">\n+<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" >\n+<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" >\n+<note label="description">tr|O16132|O16132_HYDVU NK-2 class homeobox transcription factor OS=Hydra vulgaris GN=CnNK-2 PE=2 SV=1</note>\n+<file type="peptide" URL="/Users/icooke/Desktop/iptest/AASequences.fasta"/>\n+<peptide start="1" end="328">\n+\t\n+<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">\n+</domain>\n+</peptide>\n+</protein>\n+</group>\n+<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" >\n+<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" >\n+<note label="description">sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1</note>\n+<file type="peptide" URL="/Users/icooke/Desktop/iptest/AASequences.fasta"/>\n+<peptide start="1" end="741">\n+\t\n+<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" b_ions="5" pre="NHAQ" post="SKKD" seq="EQSSEENFCR" missed_cleavages="0">\n+</domain>\n+</peptide>\n+</protein>\n+</group>\n+<group id="3" mh="1399.715504" z="2" rt="" expect="9.9e-02" label="tr|Q90853|Q90853_CHICK Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1" type="model" sumI="3.56" maxI="786" fI="7.86" act="0" >\n+<protein expect="-1.0" id="3.1" uid="16" label="tr|Q90853|Q90853_CHICK Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1" sumI="4.91" >\n+<note label="description">tr|Q90853|Q90853_CHICK Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1</note>\n+<file type="peptide" URL="/Users/icooke/Desktop/iptest/AASequences.fasta"/>\n+<peptide start="1" end="368">\n+\t\n+<domain id="3.1.1" start="208" end="219" expect="9.9e-02" mh="1381.663" delta="18.052" hyperscore="23.9" nextscore="19.3" y_score="7.6" y_ions="5" b_score="9.6" b_ions="4" pre="VFSR" post="KRYL" seq="SQVFQLESTFDV" missed_cleavages="0">\n+</domain>\n+</peptide>\n+</protein>\n+</group>\n+<group id="4" mh="1452.636818" z="3" rt="" expect="2.2e+00" label="sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2..." type="model" sumI="3.39" maxI="389" fI="3.89" act="0" >\n+<protein expect="0.0" id="4.1" uid="19" label="sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2..." sumI="5.26" >\n+<note label="description">sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1</note>\n+<file type="peptide" URL="/Users/icooke/Desktop/iptest/AASequences.fasta"/>\n+<peptide start="1" end="741">\n+\t\n+<domain id="4.1.1" start="589" end="600" expect="2.2e+00" mh="1413.614" delta="39.022" hyperscore="20.2" nextscore="19.4" y_score="10.9" y_ions="4" b_score="9.6" b_ions="3" pre="NNFK" post="FNEL" seq="SMLPGNFENPYF" missed_cleavages="0">\n+<aa type="M" at="590" modified="15.99492" />\n+</domain>\n+</peptide>\n+</protein>\n+</group>\n+<group id="5" mh="1399.717238" z="3" rt="" expect="1.1e+00" label="sp|O93590|ZAX_XENLA Homeobox protein zampogna OS=Xenopus laevis GN=zax PE=2 SV=1" type="model" sumI="4.15" maxI="2944" fI="29.44" act="0" >\n+<protein expect="0.0" id="5.1" uid="15" lab'..b'ites">2</note>\n+\t<note type="input" label="scoring, minimum ion count">4</note>\n+\t<note type="input" label="scoring, x ions">no</note>\n+\t<note type="input" label="scoring, y ions">yes</note>\n+\t<note type="input" label="scoring, z ions">no</note>\n+\t<note type="input" label="spectrum, dynamic range">100.0</note>\n+\t<note type="input" label="spectrum, fragment mass type">monoisotopic</note>\n+\t<note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note>\n+\t<note type="input" label="spectrum, fragment monoisotopic mass error units">Daltons</note>\n+\t<note type="input" label="spectrum, maximum parent charge">5</note>\n+\t<note type="input" label="spectrum, minimum fragment mz">50.0</note>\n+\t<note type="input" label="spectrum, minimum parent m+h">600.0</note>\n+\t<note type="input" label="spectrum, minimum peaks">6</note>\n+\t<note type="input" label="spectrum, parent monoisotopic mass error minus">100.0</note>\n+\t<note type="input" label="spectrum, parent monoisotopic mass error plus">100.0</note>\n+\t<note type="input" label="spectrum, parent monoisotopic mass error units">Daltons</note>\n+\t<note type="input" label="spectrum, parent monoisotopic mass isotope error">no</note>\n+\t<note type="input" label="spectrum, path">/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8167.d.mgf</note>\n+\t<note type="input" label="spectrum, sequence batch size">1000</note>\n+\t<note type="input" label="spectrum, threads">1</note>\n+\t<note type="input" label="spectrum, total peaks">50</note>\n+\t<note type="input" label="spectrum, use conditioning">yes</note>\n+\t<note type="input" label="spectrum, use noise suppression">no</note>\n+</group>\n+<group label="unused input parameters" type="parameters">\n+\t<note type="input" label="protein, use minimal annotations">yes</note>\n+\t<note type="input" label="refine, modification mass"></note>\n+\t<note type="input" label="refine, point mutations">no</note>\n+\t<note type="input" label="refine, potential C-terminus modifications"></note>\n+\t<note type="input" label="refine, potential N-terminus modifications"></note>\n+\t<note type="input" label="refine, potential modification mass"></note>\n+\t<note type="input" label="refine, potential modification motif"></note>\n+\t<note type="input" label="refine, tic percent">10</note>\n+\t<note type="input" label="refine, unanticipated cleavage">no</note>\n+\t<note type="input" label="refine, use potential modifications for full refinement">no</note>\n+\t<note type="input" label="scoring, pluggable scoring">no</note>\n+\t<note type="input" label="spectrum, maximum parent m+h">4000.0</note>\n+</group>\n+<group label="performance parameters" type="parameters">\n+\t<note label="list path, sequence source #1">/Users/icooke/Desktop/iptest/AASequences.fasta</note>\n+\t<note label="list path, sequence source description #1">no description</note>\n+\t<note label="modelling, duplicate peptide ids">0</note>\n+\t<note label="modelling, duplicate proteins">0</note>\n+\t<note label="modelling, total peptides used">528901</note>\n+\t<note label="modelling, total proteins used">33</note>\n+\t<note label="modelling, total spectra used">118</note>\n+\t<note label="process, start time">2014:06:22:13:57:04</note>\n+\t<note label="process, version">X! Tandem Sledgehammer (2013.09.01.1)</note>\n+\t<note label="quality values">6 7 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0</note>\n+\t<note label="refining, # input models">0</note>\n+\t<note label="refining, # input spectra">0</note>\n+\t<note label="refining, # partial cleavage">0</note>\n+\t<note label="refining, # point mutations">0</note>\n+\t<note label="refining, # potential C-terminii">0</note>\n+\t<note label="refining, # potential N-terminii">0</note>\n+\t<note label="refining, # unanticipated cleavage">0</note>\n+\t<note label="timing, initial modelling total (sec)">0.61</note>\n+\t<note label="timing, initial modelling/spectrum (sec)">0.0052</note>\n+\t<note label="timing, load sequence models (sec)">0.00</note>\n+\t<note label="timing, refinement/spectrum (sec)">0.0000</note>\n+</group>\n+</bioml>\n' |
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| diff -r c60d1f18fd85 -r 9d6e0ad4d600 test-data/testdb.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testdb.fasta Thu Mar 26 19:53:53 2015 -0400 |
| b |
| @@ -0,0 +1,38 @@ +>sp|ALBU_BOVIN| +MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIA +FSQYLQQCPFDEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCK +VASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEF +KADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGAC +LLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAE +FVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE +CCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFL +GSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKL +KHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVS +RSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCC +TESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQT +ALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVV +STQTALA +>sp|AMYS_HUMAN| +MKLFWLLFTIGFCWAQYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPK +GFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTR +CNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWD +FNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNH +LIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVI +DLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWG +FMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGF +TRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCE +HRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWT +FSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAED +PFIAIHAESKL +>sp|CAS1_BOVIN| +MKLLILTCLVAVALARPKHPIKHQGLPQEVLNENLLRFFVAPFPEVFGKE +KVNELSKDIGSESTEDQAMEDIKQMEAESISSSEEIVPNSVEQKHIQKED +VPSERYLGYLEQLLRLKKYKVPQLEIVPNSAEERLHSMKEGIHAQQKEPM +IGVNQELAYFYPELFRQFYQLDAYPSGAWYYVPLGTQYTDAPSFSDIPNP +IGSENSEKTTMPLW +>sp|CAS2_BOVIN| +MKFFIFTCLLAVALAKNTMEHVSSSEESIISQETYKQEKNMAINPSKENL +CSTFCKEVVRNANEEEYSIGSSSEESAEVATEEVKITVDDKHYQKALNEI +NQFYQKFPQYLQYLYQGPIVLNPWDQVKRNAVPITPTLNREQLSTSEENS +KKTVDMESTEVFTKKTKLTEEEKNRLNFLKKISQRYQKFALPQYLKTVYQ +HQKAMKPWIQPKTKVIPYVRYL \ No newline at end of file |
| b |
| diff -r c60d1f18fd85 -r 9d6e0ad4d600 test-data/tiny.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tiny.mzML Thu Mar 26 19:53:53 2015 -0400 |
| b |
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| diff -r c60d1f18fd85 -r 9d6e0ad4d600 tool-data/tandem_mods.loc.sample --- a/tool-data/tandem_mods.loc.sample Tue Jul 01 11:06:33 2014 -0400 +++ b/tool-data/tandem_mods.loc.sample Thu Mar 26 19:53:53 2015 -0400 |
| [ |
| @@ -3,4 +3,5 @@ # 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 +Oxidation M oxidation_m_ 15.994915@M oxidation_m_ +Biotin K biotin_k_ 226.077598@K biotin_k_ \ No newline at end of file |