Mercurial > repos > galaxyp > openms_psmfeatureextractor
changeset 0:16a3498124d1 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
| author | galaxyp |
|---|---|
| date | Mon, 12 Feb 2018 13:40:23 -0500 |
| parents | |
| children | 064ff75dd79c |
| files | PSMFeatureExtractor.xml filetypes.txt macros.xml readme.md test-data/DecoyDatabase_input.fasta test-data/DecoyDatabase_output.fasta tool.conf tools_blacklist.txt |
| diffstat | 8 files changed, 908 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PSMFeatureExtractor.xml Mon Feb 12 13:40:23 2018 -0500 @@ -0,0 +1,89 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> +<!--Proposed Tool Section: [Utilities]--> +<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="2.3.0"> + <description>Computes extra features for each input PSM.</description> + <macros> + <token name="@EXECUTABLE@">PSMFeatureExtractor</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>PSMFeatureExtractor + +-in + #for token in $param_in: + $token + #end for +#if $param_out: + -out $param_out +#end if + +#if $rep_param_extra: +-extra + #for token in $rep_param_extra: + #if " " in str(token): + "$token.param_extra" + #else + $token.param_extra + #end if + #end for +#end if +#if $param_multiple_search_engines: + -multiple_search_engines +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_skip_db_check: + -skip_db_check +#end if + #if $adv_opts.param_concat: + -concat +#end if + #if $adv_opts.param_impute: + -impute +#end if + #if $adv_opts.param_limit_imputation: + -limit_imputation +#end if + #if $adv_opts.param_force: + -force +#end if +#end if +</command> + <inputs> + <param name="param_in" type="data" format="mzid,idxml" multiple="true" optional="False" size="30" label="Input file(s)" help="(-in) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <repeat name="rep_param_extra" min="0" title="param_extra"> + <param name="param_extra" type="text" size="30" label="List of the MetaData parameters to be included in a feature set for precolato" help="(-extra) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param name="param_multiple_search_engines" display="radio" type="boolean" truevalue="-multiple_search_engines" falsevalue="" checked="false" optional="True" label="Combine PSMs from different search engines by merging on scan level" help="(-multiple_search_engines) "/> + <expand macro="advanced_options"> + <param name="param_skip_db_check" display="radio" type="boolean" truevalue="-skip_db_check" falsevalue="" checked="false" optional="True" label="Manual override to skip the check if same settings for multiple search engines were applied" help="(-skip_db_check) Only valid together with -multiple_search_engines flag"/> + <param name="param_concat" display="radio" type="boolean" truevalue="-concat" falsevalue="" checked="false" optional="True" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="(-concat) Only valid together with -multiple_search_engines flag"/> + <param name="param_impute" display="radio" type="boolean" truevalue="-impute" falsevalue="" checked="false" optional="True" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="(-impute) Only valid together with -multiple_search_engines flag"/> + <param name="param_limit_imputation" display="radio" type="boolean" truevalue="-limit_imputation" falsevalue="" checked="false" optional="True" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="(-limit_imputation) Only valid together with -multiple_search_engines flag"/> + <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + </expand> + </inputs> + <outputs> + <data name="param_out" metadata_source="param_in" format="input"/> + </outputs> + <help>Computes extra features for each input PSM. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_PSMFeatureExtractor.html</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filetypes.txt Mon Feb 12 13:40:23 2018 -0500 @@ -0,0 +1,29 @@ +# CTD type # Galaxy type # Long Galaxy data type # Mimetype +csv tabular galaxy.datatypes.tabular:Tabular +fasta fasta galaxy.datatypes.sequence:Fasta +FASTA fasta galaxy.datatypes.sequence:Fasta +ini txt galaxy.datatypes.data:Text +txt txt galaxy.datatypes.data:Text +options txt galaxy.datatypes.data:Text +grid grid galaxy.datatypes.data:Grid +html html galaxy.datatypes.text:Html text/html +HTML html galaxy.datatypes.text:Html text/html +TraML traml galaxy.datatypes.proteomics:TraML application/xml +traML traml galaxy.datatypes.proteomics:TraML application/xml +XML xml galaxy.datatypes.xml:GenericXml application/xml +consensusXML consensusxml galaxy.datatypes.proteomics:ConsensusXML application/xml +edta tabular galaxy.datatypes.tabular:Tabular +featureXML featurexml galaxy.datatypes.proteomics:FeatureXML application/xml +idXML idxml galaxy.datatypes.proteomics:IdXML application/xml +mzML mzml galaxy.datatypes.proteomics:MzML application/xml +mzXML mzxml galaxy.datatypes.proteomics:MzXML application/xml +pepXML pepxml galaxy.datatypes.proteomics:PepXml application/xml +qcML qcml galaxy.datatypes.xml:GenericXml application/xml +trafoXML trafoxml galaxy.datatypes.xml:GenericXml application/xml +tsv tabular galaxy.datatypes.tabular:Tabular +xsd txt galaxy.datatypes.data:Text +mzq mzq galaxy.datatypes.proteomics:MzQuantML application/xml +msp msp galaxy.datatypes.proteomics:Msp +mzid mzid galaxy.datatypes.proteomics:MzIdentML application/xml +png png galaxy.datatypes.images:Png image/png +mgf mgf galaxy.datatypes.proteomics:Mgf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Feb 12 13:40:23 2018 -0500 @@ -0,0 +1,36 @@ +<?xml version='1.0' encoding='UTF-8'?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.3">openms</requirement> + <requirement type="package" version="15.12.15.2">xtandem</requirement> + <requirement type="package" version="1.0">fido</requirement> + <requirement type="package" version="2017.07.21">msgf_plus</requirement> + <yield/> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <regex match="Exception:"/> + </stdio> + </xml> + <xml name="references"> + <citations> + <citation type="doi">doi:10.1186/1471-2105-9-163</citation> + </citations> + </xml> + <xml name="advanced_options"> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic"/> + <when value="advanced"> + <yield/> + </when> + </conditional> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.md Mon Feb 12 13:40:23 2018 -0500 @@ -0,0 +1,211 @@ +Galaxy wrapper for OpenMS +========================= + +OpenMS is an open-source software C++ library for LC/MS data management and analyses. +It offers an infrastructure for the rapid development of mass spectrometry related software. +OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux. + +More informations are available at: + + * https://github.com/OpenMS/OpenMS + * http://open-ms.sourceforge.net + + +Generating OpenMS wrappers +========================== + + * install OpenMS (you can do this automatically through Conda) + * create a folder called CTD + * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory: + + ```bash + for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; + ``` + + * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow: + + ```bash + ls >> tools.txt + ``` + + * search for the `bin` folder of your conda environment containing OpenMS and do: + + ```bash + while read p; do + ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD; + done <tools.txt + ``` + + * You should have all CTD files now. `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). + + * clone or install CTDopts + + ```bash + git clone https://github.com/genericworkflownodes/CTDopts + ``` + + * add CTDopts to your `$PYTHONPATH` + + ```bash + export PYTHONPATH=/home/user/CTDopts/ + ``` + + * clone or install CTD2Galaxy + + ```bash + git clone https://github.com/WorkflowConversion/CTDConverter.git + ``` + + * If you have CTDopts and CTDConverter installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. Further information can be found on the CTDConverter page. + + ```bash + python convert.py galaxy \ + -i /PATH/TO/YOUR/CTD/*.ctd \ + -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ + -d datatypes_conf.xml -g openms \ + -b version log debug test no_progress threads \ + in_type executable myrimatch_executable \ + fido_executable fidocp_executable \ + omssa_executable pepnovo_e xecutable \ + xtandem_executable param_model_directory \ + java_executable java_memory java_permgen \ + r_executable rt_concat_trafo_out param_id_pool \ + -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ + -s PATH/TO/tools_blacklist.txt + ``` + + + * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. Some of these tools might already be deprecated and the files might not exist: + + ``` + sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml + sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml + sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml + sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml + sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml + ``` + + * For some tools, additional work has to be done. In `MSGFPlusAdapter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): + + ``` + <command><![CDATA[ + + ## check input file type + #set $in_type = $param_in.ext + + ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files + ln -s '$param_in' 'param_in.${in_type}' && + ln -s '$param_database' param_database.fasta && + ## find location of the MSGFPlus.jar file of the msgf_plus conda package + MSGF_JAR=\$(msgf_plus -get_jar_path) && + + MSGFPlusAdapter + -executable \$MSGF_JAR + #if $param_in: + -in 'param_in.${in_type}' + #end if + #if $param_out: + -out $param_out + #end if + #if $param_mzid_out: + -mzid_out $param_mzid_out + #end if + #if $param_database: + -database param_database.fasta + #end if + + [...] + ]]> + ``` + + * In Xtandem Converter and probably in others: + + ``` + #if str($param_missed_cleavages) != '': + ``` + This is because integers needs to be compared as string otherwise `0` becomes `false`. + + * In `MetaProSIP.xml` add `R` as a requirement: + + ``` + <expand macro="requirements"> + <requirement type="package" version="3.3.1">r-base</requirement> + </expand> + ``` + + * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): + + ``` + <command><![CDATA[ + + ## check input file type + #set $in_type = $param_in.ext + + ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files + ln -s '$param_in' 'param_in.${in_type}' && + + IDFileConverter + + #if $param_in: + -in 'param_in.${in_type}' + #end if + + [...] + ]]> + ``` + + * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.: + + - `<data name="param_out" auto_format="true"/>` + - `<data name="param_out" metadata_source="param_in" auto_format="true"/>` + + * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files. + + ``` + <tests> + <test> + <param name="param_in" value="DecoyDatabase_input.fasta"/> + <output name="param_out" file="DecoyDatabase_output.fasta"/> + </test> + </tests> + ``` + + + * `This section might not be up to date. It might be worth trying if these tools will run now.` These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in + by the automatic conversion step and are therefore in `tools_blacklist.txt`: + * SeedListGenerator + * SpecLibSearcher + * MapAlignerIdentification + * MapAlignerPoseClustering + * MapAlignerSpectrum + * MapAlignerRTTransformer + + * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well: + * OMSSAAdapter + * MyrimatchAdapter + + * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed: + * PepNovoAdapter + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. +
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+IVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLAALTRNSINLLPNHLAQALHV +QSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF +IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINE +TYLARNVIIFASILINFLGAILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTG +VLAMVTCAVFLRLNSVLKLAVLLIMIAIYALLTETVYAGLFLRYDNLNHSGEDFLGTKEV +SLLLMAMFLLAVFYHGQQLEYTARLDFLWRVQAKEEINEMKELREHNENMLRNILPSHVA +RHFLEKDRDNEELYSQSYDAVGVMFASIPGFADFYSQTEMNNQGVECLRLLNEIIADFDE +LLGEDRFQDIEKIKTIGSTYMAVSGLSPEKQQCEDKWGHLCALADFSLALTESIQEINKH +SFNNFELRIGISHGSVVAGVIGAKKPQYDIWGKTVNLASRMDSTGVSGRIQVPEETYLIL +KDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV +QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP +>143 +MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQ +LNSIQKNHVHIANPDFIWKSIREKRLLDVKNYDPYKPLDITPPPDQKASSSEVKTEGLCP +DSATEEEDTVELTEFGMQNVEIPHLPQDFEVAKYNTLEKVGMEGGQEAVVVELQCSRDSR +DCPFLISSHFLLDDGMETRRQFAIKKTSEDASEYFENYIEELKKQGFLLREHFTPEATQL +ASEQLQALLLEEVMNSSTLSQEVSDLVEMIWAEALGHLEHMLLKPVNRISLNDVSKAEGI +LLLVKAALKNGETAEQLQKMMTEFYRLIPHKGTMPKEVNLGLLAKKADLCQLIRDMVNVC +ETNLSKPNPPSLAKYRALRCKIEHVEQNTEEFLRVRKEVLQNHHSKSPVDVLQIFRVGRV +NETTEFLSKLGNVRPLLHGSPVQNIVGILCRGLLLPKVVEDRGVQRTDVGNLGSGIYFSD +SLSTSIKYSHPGETDGTRLLLICDVALGKCMDLHEKDFSLTEAPPGYDSVHGVSQTASVT +TDFEDDEFVVYKTNQVKMKYIIKFSMPGDQIKDFHPSDHTELEEYRPEFSNFSKVEDYQL +PDAKTSSSTKAGLQDASGNLVPLEDVHIKGRIIDTVAQVIVFQTYTNKSHVPIEAKYIFP +LDDKAAVCGFEAFINGKHIVGEIKEKEEAQQEYLEAVTQGHGAYLMSQDAPDVFTVSVGN +LPPKAKVLIKITYITELSILGTVGVFFMPATVAPWQQDKALNENLQDTVEKICIKEIGTK +QSFSLTMSIEMPYVIEFIFSDTHELKQKRTDCKAVISTMEGSSLDSSGFSLHIGLSAAYL +PRMWVEKHPEKESEACMLVFQPDLDVDLPDLASESEVIICLDCSSSMEGVTFLQAKQIAL +HALSLVGEKQKVNIIQFGTGYKELFSYPKHITSNTMAAEFIMSATPTMGNTDFWKTLRYL +SLLYPARGSRNILLVSDGHLQDESLTLQLVKRSRPHTRLFACGIGSTANRHVLRILSQCG +AGVFEYFNAKSKHSWRKQIEDQMTRLCSPSCHSVSVKWQQLNPDVPEALQAPAQVPSLFL +NDRLLVYGFIPHCTQATLCALIQEKEFRTMVSTTELQKTTGTMIHKLAARALIRDYEDGI +LHENETSHEMKKQTLKSLIIKLSKENSLITQFTSFVAVEKRDENESPFPDIPKVSELIAK +EDVDFLPYMSWQGEPQEAVRNQSLLASSEWPELRLSKRKHRKIPFSKRKMELSQPEVSED +FEEDGLGVLPAFTSNLERGGVEKLLDLSWTESCKPTATEPLFKKVSPWETSTSSFFPILA +PAVGSYLPPTARAHSPASLSFASYRQVASFGSAAPPRQFDASQFSQGPVPGTCADWIPQS +ASCPTGPPQNPPSSPYCGIVFSGSSLSSAQSAPLQHPGGFTTRPSAGTFPELDSPQLHFS +LPTDPDPIRGFGSYHPSASSPFHFQPSAASLTANLRLPMASALPEALCSQSRTTPVDLCL +LEESVGSLEGSRCPVFAFQSSDTESDELSEVLQDSCFLQIKCDTKDDSILCFLEVKEEDE +IVCIQHWQDAVPWTELLSLQTEDGFWKLTPELGLILNLNTNGLHSFLKQKGIQSLGVKGR +ECLLDLIATMLVLQFIRTRLEKEGIVFKSLMKMDDASISRNIPWAFEAIKQASEWVRRTE +GQYPSICPRLELGNDWDSATKQLLGLQPISTVSPLHRVLHYSQG +>213 +MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF +EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP +ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF +FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV +ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK +ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR +RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE +QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV +LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL +SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV +AASQAALGL +>230 +MPHSYPALSAEQKKELSDIALRIVAPGKGILAADESVGSMAKRLSQIGVENTEENRRLYR +QVLFSADDRVKKCIGGVIFFHETLYQKDDNGVPFVRTIQDKGIVVGIKVDKGVVPLAGTD +GETTTQGLDGLSERCAQYKKDGADFAKWRCVLKISERTPSALAILENANVLARYASICQQ +NGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHVYLEGTLLKPNMVTPGHAC +PIKYTPEEIAMATVTALRRTVPPAVPGVTFLSGGQSEEEASFNLNAINRCPLPRPWALTF +SYGRALQASALNAWRGQRDNAGAATEEFIKRAEVNGLAAQGKYEGSGEDGGAAAQSLYIA +NHAY +>231 +MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQ +EKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGK +EFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKP +AVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAK +HNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCA +LLSCTSHKDYPFHEEF +>242 +MATYKVRVATGTDLLSGTRDSISLTIVGTQGESHKQLLNHFGRDFATGAVGQYTVQCPQD +LGELIIIRLHKERYAFFPKDPWYCNYVQICAPNGRIYHFPAYQWMDGYETLALREATGKT +TADDSLPVLLEHRKEEIRAKQDFYHWRVFLPGLPSYVHIPSYRPPVRRHRNPNRPEWNGY +IPGFPILINFKATKFLNLNLRYSFLKTASFFVRLGPMALAFKVRGLLDCKHSWKRLKDIR +KIFPGKKSVVSEYVAEHWAEDTFFGYQYLNGVNPGLIRRCTRIPDKFPVTDDMVAPFLGE +GTCLQAELEKGNIYLADYRIMEGIPTVELSGRKQHHCAPLCLLHFGPEGKMMPIAIQLSQ +TPGPDCPIFLPSDSEWDWLLAKTWVRYAEFYSHEAIAHLLETHLIAEAFCLALLRNLPMC +HPLYKLLIPHTRYTVQINSIGRAVLLNEGGLSAKGMSLGVEGFAGVMVRALSELTYDSLY +LPNDFVERGVQDLPGYYYRDDSLAVWNALEKYVTEIITYYYPSDAAVEGDPELQSWVQEI +FKECLLGRESSGFPRCLRTVPELIRYVTIVIYTCSAKHAAVNTGQMEFTAWMPNFPASMR +NPPIQTKGLTTLETFMDTLPDVKTTCITLLVLWTLSREPDDRRPLGHFPDIHFVEEAPRR +SIEAFRQRLNQISHDIRQRNKCLPIPYYYLDPVLIENSISI
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DecoyDatabase_output.fasta Mon Feb 12 13:40:23 2018 -0500 @@ -0,0 +1,228 @@ +>12 +MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI +STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL +YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM +VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR +DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL +MIIVPTDTQNIFFMSKVTNPKQA +>18 +MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMKQLNIIQNAEAVHFFCNYEES +RGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQNASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLIT +MACGSCSNENALKTIFMWYRSKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS +FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGGDNHASDDFFRKLRDIARKHG +CAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMMTGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIK +REDLLNNAAHAGKALLTGLLDLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF +RDHHAHLFLNIFSDILADFK +>88 +MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVIS +GERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLW +CQRKTAPYRNVNIQNFHTSWKDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP +DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRTIPWLENRTPEKTMQAMQKKL +EDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAFMPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLE +HLAEKFRQKASTHETWAYGKEQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN +DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQDMFIVHSIEEIQSLITAHEQ +FKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYSTVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRR +QFAAQANAIGPWIQNKMEEIARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI +RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRACLISMGYDLGEAEFARIMTL +VDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILASDKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALD +YAAFSSALYGESDL +>112 +MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGPPRCPWQDDAFIRRGGPGKGK +ELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWRRLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLV +LLTAVLLAFHAAPARPQPAYVALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW +CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTNVIGICTHYPAEVSQRQAFQE +TRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINTKKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQEL +VMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV +HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNAYLKEQHIETFLILGASQKRK +EEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFRQMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQL +RKDHVRRFLLTFQREDLEKKYSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC +GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLTPADITACHLQQLNYSLGLDA +PLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLAMIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNET +FDGLDCPAAGRVALKYMTPVILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF +LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAA +SGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDST +GVPDRIQVTTDLYQVLAAKGYQLECRGVVKVKGKGEMTTYFLNGGPSS +>114 +MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGSGSGGSGKASDPAGGGPNHHA +PQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASGSGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNS +FKSRDLERLYQRYFLGQRRKSEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT +YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTSLLQVILQVVIPRLAVISINQ +VVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEARLRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQH +QFHRIYIHRYENVSILFADVKGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH +CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKLESGGIPGRIHISKATLDCLN +GDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPEDIVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLA +ALTRNSINLLPNHLAQALHVQSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF +IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINETYLARNVIIFASILINFLGA +ILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTGVLAMVTCAVFLRLNSVLKLAVLLIMIAIYALLTETVYAGL +FLRYDNLNHSGEDFLGTKEVSLLLMAMFLLAVFYHGQQLEYTARLDFLWRVQAKEEINEMKELREHNENMLRNILPSHVA +RHFLEKDRDNEELYSQSYDAVGVMFASIPGFADFYSQTEMNNQGVECLRLLNEIIADFDELLGEDRFQDIEKIKTIGSTY +MAVSGLSPEKQQCEDKWGHLCALADFSLALTESIQEINKHSFNNFELRIGISHGSVVAGVIGAKKPQYDIWGKTVNLASR +MDSTGVSGRIQVPEETYLILKDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV +QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP +>143 +MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQLNSIQKNHVHIANPDFIWKS +IREKRLLDVKNYDPYKPLDITPPPDQKASSSEVKTEGLCPDSATEEEDTVELTEFGMQNVEIPHLPQDFEVAKYNTLEKV +GMEGGQEAVVVELQCSRDSRDCPFLISSHFLLDDGMETRRQFAIKKTSEDASEYFENYIEELKKQGFLLREHFTPEATQL +ASEQLQALLLEEVMNSSTLSQEVSDLVEMIWAEALGHLEHMLLKPVNRISLNDVSKAEGILLLVKAALKNGETAEQLQKM +MTEFYRLIPHKGTMPKEVNLGLLAKKADLCQLIRDMVNVCETNLSKPNPPSLAKYRALRCKIEHVEQNTEEFLRVRKEVL +QNHHSKSPVDVLQIFRVGRVNETTEFLSKLGNVRPLLHGSPVQNIVGILCRGLLLPKVVEDRGVQRTDVGNLGSGIYFSD +SLSTSIKYSHPGETDGTRLLLICDVALGKCMDLHEKDFSLTEAPPGYDSVHGVSQTASVTTDFEDDEFVVYKTNQVKMKY +IIKFSMPGDQIKDFHPSDHTELEEYRPEFSNFSKVEDYQLPDAKTSSSTKAGLQDASGNLVPLEDVHIKGRIIDTVAQVI +VFQTYTNKSHVPIEAKYIFPLDDKAAVCGFEAFINGKHIVGEIKEKEEAQQEYLEAVTQGHGAYLMSQDAPDVFTVSVGN +LPPKAKVLIKITYITELSILGTVGVFFMPATVAPWQQDKALNENLQDTVEKICIKEIGTKQSFSLTMSIEMPYVIEFIFS +DTHELKQKRTDCKAVISTMEGSSLDSSGFSLHIGLSAAYLPRMWVEKHPEKESEACMLVFQPDLDVDLPDLASESEVIIC +LDCSSSMEGVTFLQAKQIALHALSLVGEKQKVNIIQFGTGYKELFSYPKHITSNTMAAEFIMSATPTMGNTDFWKTLRYL +SLLYPARGSRNILLVSDGHLQDESLTLQLVKRSRPHTRLFACGIGSTANRHVLRILSQCGAGVFEYFNAKSKHSWRKQIE +DQMTRLCSPSCHSVSVKWQQLNPDVPEALQAPAQVPSLFLNDRLLVYGFIPHCTQATLCALIQEKEFRTMVSTTELQKTT +GTMIHKLAARALIRDYEDGILHENETSHEMKKQTLKSLIIKLSKENSLITQFTSFVAVEKRDENESPFPDIPKVSELIAK +EDVDFLPYMSWQGEPQEAVRNQSLLASSEWPELRLSKRKHRKIPFSKRKMELSQPEVSEDFEEDGLGVLPAFTSNLERGG +VEKLLDLSWTESCKPTATEPLFKKVSPWETSTSSFFPILAPAVGSYLPPTARAHSPASLSFASYRQVASFGSAAPPRQFD +ASQFSQGPVPGTCADWIPQSASCPTGPPQNPPSSPYCGIVFSGSSLSSAQSAPLQHPGGFTTRPSAGTFPELDSPQLHFS +LPTDPDPIRGFGSYHPSASSPFHFQPSAASLTANLRLPMASALPEALCSQSRTTPVDLCLLEESVGSLEGSRCPVFAFQS +SDTESDELSEVLQDSCFLQIKCDTKDDSILCFLEVKEEDEIVCIQHWQDAVPWTELLSLQTEDGFWKLTPELGLILNLNT +NGLHSFLKQKGIQSLGVKGRECLLDLIATMLVLQFIRTRLEKEGIVFKSLMKMDDASISRNIPWAFEAIKQASEWVRRTE +GQYPSICPRLELGNDWDSATKQLLGLQPISTVSPLHRVLHYSQG +>213 +MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVAD +ESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLK +KYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV +ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVEND +EMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDE +FKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV +LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHK +PKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALGL +>230 +MPHSYPALSAEQKKELSDIALRIVAPGKGILAADESVGSMAKRLSQIGVENTEENRRLYRQVLFSADDRVKKCIGGVIFF +HETLYQKDDNGVPFVRTIQDKGIVVGIKVDKGVVPLAGTDGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKISERTPS +ALAILENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHVYLEGTLLKPNMVTPGHAC +PIKYTPEEIAMATVTALRRTVPPAVPGVTFLSGGQSEEEASFNLNAINRCPLPRPWALTFSYGRALQASALNAWRGQRDN +AGAATEEFIKRAEVNGLAAQGKYEGSGEDGGAAAQSLYIANHAY +>231 +MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLW +CTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGIS +NFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAK +HNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF +>242 +MATYKVRVATGTDLLSGTRDSISLTIVGTQGESHKQLLNHFGRDFATGAVGQYTVQCPQDLGELIIIRLHKERYAFFPKD +PWYCNYVQICAPNGRIYHFPAYQWMDGYETLALREATGKTTADDSLPVLLEHRKEEIRAKQDFYHWRVFLPGLPSYVHIP +SYRPPVRRHRNPNRPEWNGYIPGFPILINFKATKFLNLNLRYSFLKTASFFVRLGPMALAFKVRGLLDCKHSWKRLKDIR +KIFPGKKSVVSEYVAEHWAEDTFFGYQYLNGVNPGLIRRCTRIPDKFPVTDDMVAPFLGEGTCLQAELEKGNIYLADYRI +MEGIPTVELSGRKQHHCAPLCLLHFGPEGKMMPIAIQLSQTPGPDCPIFLPSDSEWDWLLAKTWVRYAEFYSHEAIAHLL +ETHLIAEAFCLALLRNLPMCHPLYKLLIPHTRYTVQINSIGRAVLLNEGGLSAKGMSLGVEGFAGVMVRALSELTYDSLY +LPNDFVERGVQDLPGYYYRDDSLAVWNALEKYVTEIITYYYPSDAAVEGDPELQSWVQEIFKECLLGRESSGFPRCLRTV +PELIRYVTIVIYTCSAKHAAVNTGQMEFTAWMPNFPASMRNPPIQTKGLTTLETFMDTLPDVKTTCITLLVLWTLSREPD +DRRPLGHFPDIHFVEEAPRRSIEAFRQRLNQISHDIRQRNKCLPIPYYYLDPVLIENSISI +>DECOY_12 +AQKPNTVKSMFFINQTDTPVIIMLFPRNFRVITRTEVLASLLTIKVATAASAETGEEFVDLVAKHVVQSVALNRAGTIGS +LDAKSTFAEEIGLQLLIDNLNYDRSISFKPLYLEGIERFELSDRWRKLTEPLLMAEVEEMKDQDPLIFLASANGTYKLEV +VTCSLEEDRFYPITLHHLSMMPVMVWKKKSLYFRSQHTDQPDFPMEWKAKFFIYNVLVMMTQSDLDKILDTIKGRTGNKV +YDNILKKAAASDQFDTAFAESGYLRKADETFRDLLSLQEKVFMANGMSLQLEDSSQNLTRLLHQFSQHIEAESTETLNFK +LGKLIETLTTNHAGLSLFALATSISLPSFIVNKDPAKLVLQKYLSFAFDVNASALGLDVHTGRDQNEQTLNEEDLPSNPH +CLVAPCFGAALLGLALLPLMREM +>DECOY_18 +KFDALIDSFINLFLHAHHDRFVLTPRFRISKDGCGGLVVGKNRAILILKNRISDDPTDFSCFTGRGRVRSIFQPYRAQLD +LLGTLLAKGAHAANNLLDERKIINIVEALLLNKSPDGLWTNFIRYPANPRFEEKHFFGGTMMKKSFTMVDAPDDLGWHEH +AWFKGTCGGGTQVEDVLFACGHKRAIDRLKRFFDDSAHNDGGESQIPEVIIGAVTKKKKRYKVILDEVEELCRAEEQQNE +KVFEELPYKLRPFPAIPWDFSPIDIKHIAKSHTTALCGMTRGHFAGMFSLISYDPCGPAQNIMCTELEEQSFGRQGREKS +RYWMFITKLANENSCSGCAMTILQSMGKPAVSLLSQRLKEVFNEPPLIGLAPRNVFMSANQPQQILKLLAPHSYGIPVSS +IQSYLDLMRNGDVDVLYNGRSEEYNCFFHVAEANQIINLQKMLEQSRPGPVETKMLPGDYDFEVDVKAAAQSIHRSGPVL +LRYSHQFSCALRQALLMSAM +>DECOY_88 +LDSEGYLASSFAAYDLAGPVSGPGSYAPMRKICYQAQDPPLERRLEEALIYPKDSALIRFSAIVQEATDTDATERTMFDI +FSQFTVTGQGNPDVLTMIRAFEAEGLDYGMSILCARFDEHDMLGNKRRDFHNFSARFENMQEQTIGKADRTLIQTEVENI +TRAITTLLLEWGVRIHEMTYNTHKNDFVLAEQILQHDGELKDINNKYNIINHEYQKLQNMQDELAGTIQISSRAIEEMKN +QIWPGIANAQAAFQRRLRENAHQRALEEQLSQDRIPVLQKVKDWKTRLEDMTVTSYPNSSSIRINYSQIVKEVENQIAMI +SQREGDAEPLTAKFQEHATILSQIEEISHVIFMDQLDEMAGEMWNNFPAARKAFELHLQDITELLKEMRELAERRKQTLT +GLRDWQDCIKQCRDNVNVADHYDLENLEQAIAAIQEVRDQHAALDSEFAEHKRLLARVETLSASEYDKQLLIQEKGYAWT +EHTSAKQRFKEALHELRELRRIENLLWEEYGKEAQELRQWAGAIDSVMKGESPMFAPRNSIRLKTQLTNFNIELQCKEQV +KPPKHKRRYDRFDELKKQMAQMTKEPTRNELWPITRRIWELLESALREYEEMLRENEQNVALVKCIRNAATEAQEAGAFA +HYFCSVYTMIAREDPKPTNVIDEADLMKPIDLHKEAIEMALNINGIPDDKNLKSYDILDPRHRHILACLGLGDKWSTHFN +QINVNRYPATKRQCWLLLGEKASTEEVSIDQIAFRLIITWIMGLTMKVNGDVIEEAGISVLKVGKSAIYDLAKNVNAIKH +FRMKGRDPKPLREGSIVELLLMLKLGNRFDEEINEIQTGAKRLHSNCWATFTKRQQKEWAPDLLLDRDWEEEQIMYEDED +YVYNYQVGPEIQNM +>DECOY_112 +SSPGGNLFYTTMEGKGKVKVVGRCELQYGKAALVQYLDTTVQIRDPVGTSDMRSSVNVTNGWIDYQPKRAGIVGAVVPGM +NLGIKMQFNNFSHENIHKMQEMLRMAYDALATIHSRGVQDYTSANLGSAAMYTSGITKIKELQRFREESIIEDFDAIIEN +LLRLCEVGENNAELEVYFESFNAISAFMVAVCECSQYYLEDNRRERALFHAAVDKPLINHLLRRNYAQLEEMEEKEGTAQ +LKWLFDLRATSEVQQAHLYLALAFVLLIVPTMYKLAVRGAAPCDLGDFTENSSALGHVGLLLDYNDFITAPPGLLLLVLY +ILGLVFIMALKGISSIHLFVSSALLSLLMNGIFYEPFSCTPMTGECLPADLGLSYNLQQLHCATIDAPTLNLMRAACSRI +PTHNCTFMNAIASTFVLLVSFIGVATSHARSRVISRSLRQLAKPFLSGCSYVACILVTILLLLFISAYIGLMLTSHPFIL +LQIFCIFCFVLLACAVYAGFRPDVKRSYKKELDERQFTLLFRRVHDKRLQDISRADIARSLFEDVEDEPNLADQTGRNDK +SSDDIGMQRFAKSDKTRSFARDPVWRPMLGEMSNARTRQLKALMAKEEKRKQSAGLILFTEIHQEKLYANREGGRGPEVE +YDGNLYQLTARTIHIRGARGGAEMHNALTVDNSWVDFQWKRLGLVGCHVRGSHIGVRMNVNVGTVERVLSIAEIMDVGME +VCCHAHDARAEPLGSVCYYCDGLIKIRLCHNEAALKDFRAFLENLTMVLEQATCQSALSTFGEIDAFLISVNDHKQIYIK +HFMMDEKKTNIDEKMEMAVHQPLVSLLLREQQRNEHQLHLRAQIYGRTEQFAQRQSVEAPYHTCIGIVNTCLFLLVNAGL +QKWLFADGRNLQWALILHLTSLGLGSLVAARMRIPLLTYAIYVFFVPCWLGASPSRPDAALAGGVQVAALIGLVVYSVVW +MSDQRFSHRNCVVMLGVFLAAACALLAVYAPQPRAPAAHFALLVATLLVLVAMLLTLSSQNMQFFYRQYLRELKASRFQK +SQFVQVLRRWCSRGSRPVADPAVEATGGATTTVETDEFGLAVARLGLEKGKGPGGRRIFADDQWPCRPPGAPTPSPPEAD +RLCSMYRPTCFGGARTGRRRSRKQGNREGWATKREDVKPVLLGSFWSM +>DECOY_114 +PLDSKDTGEAQAGPETGSPSLLTRRNYHGKIIGTNNNENLLQKQRQRNLSQVLGLVVAALSYQGPLRRPPLIFPNPQVRG +LLFYTKIKGEQESIGKVYIEGRYDFAFGQDKLILYTEEPVQIRGSVGTSDMRSALNVTKGWIDYQPKKAGIVGAVVSGHS +IGIRLEFNNFSHKNIEQISETLALSFDALACLHGWKDECQQKEPSLGSVAMYTSGITKIKEIDQFRDEGLLEDFDAIIEN +LLRLCEVGQNNMETQSYFDAFGPISAFMVGVADYSQSYLEENDRDKELFHRAVHSPLINRLMNENHERLEKMENIEEKAQ +VRWLFDLRATYELQQGHYFVALLFMAMLLLSVEKTGLFDEGSHNLNDYRLFLGAYVTETLLAYIAIMILLVALKLVSNLR +LFVACTVMALVGTFVFYEPYSCIDTFVASSNFTLNKLPISKDFDCWLINLIAGLFNILISAFIIVNRALYTENIWCCTKR +LILPLCKYDEATTILVLASHLMILISFQITMPMVRSSPLLSQIATIFLLVIFACVLNSKFVEDRMQSYKHELSSDKFMLS +FPKIHERRLKDGSRLDITHEIRKNIEEPGSQVHLAQALHNPLLNISNRTLAALTNQKGVINDFPLEPSWSGETFTAGSNR +RDSSSVSEKVIDEPLSLLSDEPQKILYTEINHKRLFENREKGHGEEVNYDGNLCDLTAKSIHIRGPIGGSELKNAIDVDW +SWVDFQWKRLGLVGCLVSGSHIGIRMDVDHKTRSRVYRITKIMSLGMEVCCHAHDQRPEPLGSVCYYCDGLIKIRLCHHE +HALRDFRAFLENLMRVLEQASLTTSLNTFGKVDAFLISVNEYRHIYIRHFQHQLHEDEVNTMDNIMELVVFRPLVSLVLR +EQRQNETELRLRAEVCRRTELFAQRQARDSLYSIFIGATNMCMFLVAQAVVQNISIVALRPIVVQLIVQLLSTGLGALIA +WTLPLPLMSYTAFLTFLVYGIGDGLLGYGLGAALIQTTMAVWTVVGSYQLYTHSTTDKRVVVLACIVVEIGTFFGLLIGK +LPDMPASALSLHLVLLTLKTLVDLVNMVVESKRRQGLFYRQYLRELDRSKFSNRLTPFIVGRYSYGGNLFFDSNSPACDL +HLFGLDGGGGSGSASGSGSREPFVKTGCTSHAREGPGLSYLPLASDGSLQPAHHNPGGGAPDSAKGSGGSGSGSGGRHGH +IFRQETIHRVATQWLLRQPRSASRGDGAPPTPHITYLEESGTLCRVDSLEM +>DECOY_143 +GQSYHLVRHLPSVTSIPQLGLLQKTASDWDNGLELRPCISPYQGETRRVWESAQKIAEFAWPINRSISADDMKMLSKFVI +GEKELRTRIFQLVLMTAILDLLCERGKVGLSQIGKQKLFSHLGNTNLNLILGLEPTLKWFGDETQLSLLETWPVADQWHQ +ICVIEDEEKVELFCLISDDKTDCKIQLFCSDQLVESLEDSETDSSQFAFVPCRSGELSGVSEELLCLDVPTTRSQSCLAE +PLASAMPLRLNATLSAASPQFHFPSSASPHYSGFGRIPDPDTPLSFHLQPSDLEPFTGASPRTTFGGPHQLPASQASSLS +SGSFVIGCYPSSPPNQPPGTPCSASQPIWDACTGPVPGQSFQSADFQRPPAASGFSAVQRYSAFSLSAPSHARATPPLYS +GVAPALIPFFSSTSTEWPSVKKFLPETATPKCSETWSLDLLKEVGGRELNSTFAPLVGLGDEEFDESVEPQSLEMKRKSF +PIKRHKRKSLRLEPWESSALLSQNRVAEQPEGQWSMYPLFDVDEKAILESVKPIDPFPSENEDRKEVAVFSTFQTILSNE +KSLKIILSKLTQKKMEHSTENEHLIGDEYDRILARAALKHIMTGTTKQLETTSVMTRFEKEQILACLTAQTCHPIFGYVL +LRDNLFLSPVQAPAQLAEPVDPNLQQWKVSVSHCSPSCLRTMQDEIQKRWSHKSKANFYEFVGAGCQSLIRLVHRNATSG +IGCAFLRTHPRSRKVLQLTLSEDQLHGDSVLLINRSGRAPYLLSLYRLTKWFDTNGMTPTASMIFEAAMTNSTIHKPYSF +LEKYGTGFQIINVKQKEGVLSLAHLAIQKAQLFTVGEMSSSCDLCIIVESESALDPLDVDLDPQFVLMCAESEKEPHKEV +WMRPLYAASLGIHLSFGSSDLSSGEMTSIVAKCDTRKQKLEHTDSFIFEIVYPMEISMTLSFSQKTGIEKICIKEVTDQL +NENLAKDQQWPAVTAPMFFVGVTGLISLETIYTIKILVKAKPPLNGVSVTFVDPADQSMLYAGHGQTVAELYEQQAEEKE +KIEGVIHKGNIFAEFGCVAAKDDLPFIYKAEIPVHSKNTYTQFVIVQAVTDIIRGKIHVDELPVLNGSADQLGAKTSSST +KADPLQYDEVKSFNSFEPRYEELETHDSPHFDKIQDGPMSFKIIYKMKVQNTKYVVFEDDEFDTTVSATQSVGHVSDYGP +PAETLSFDKEHLDMCKGLAVDCILLLRTGDTEGPHSYKISTSLSDSFYIGSGLNGVDTRQVGRDEVVKPLLLGRCLIGVI +NQVPSGHLLPRVNGLKSLFETTENVRGVRFIQLVDVPSKSHHNQLVEKRVRLFEETNQEVHEIKCRLARYKALSPPNPKS +LNTECVNVMDRILQCLDAKKALLGLNVEKPMTGKHPILRYFETMMKQLQEATEGNKLAAKVLLLIGEAKSVDNLSIRNVP +KLLMHELHGLAEAWIMEVLDSVEQSLTSSNMVEELLLAQLQESALQTAEPTFHERLLFGQKKLEEIYNEFYESADESTKK +IAFQRRTEMGDDLLFHSSILFPCDRSDRSCQLEVVVAEQGGEMGVKELTNYKAVEFDQPLHPIEVNQMGFETLEVTDEEE +TASDPCLGETKVESSSAKQDPPPTIDLPKYPDYNKVDLLRKERISKWIFDPNAIHVHNKQISNLQYQSLVDANDLIIHTC +QPNLSFSFKGGNEKIDTQLKKKQQQPLYKVKLCFICNAFIGMVM +>DECOY_213 +LGLAAQSAAVLKKGEEAFCTEKDDAKCCKEVFAAFDDMVAKLQEKTAKPKHKVLEVLATQKKIQREKESLTCIDAHFTFT +EANFEKPVYTEDVELASFCPRRNVLSETCCKTVRDSVPTKEHLVCLQNLVVSLYDEACPMRKAEPHKCCKSGVKGLNRSV +EVLTPTSVQPVKKTYRVLLANQFKYEGLQEFLECNQKILNQPEEVLPKFEDFVKAYCEHPDAAACCKELTTEYTKALRLL +LVVSYDPHRRAYEYLFMGLFVDKAEAYNKCVDKSEVFDAALSPLDAPMEDNEVEAICHSKELLPKECCEKLKSSISDQNE +CIYKALDARDDACELLDGHCCETHVKTLDTVLKSVEAFEAKPFRQSLRAVAWAKFAREGFKQLSACKLRQKASSAKGEDR +LEDLKPLLCAAKDAAQCCETFAAKYRKAFFLLEPAYFYPHRRAIEYLYKKLFTEENDHFATCMVDVEPRVLRPLNPNDDK +HQLFCENREPEQKACCDAMEGYTERLTAVTCLKDGFLTHLSKDCNEASEDAVCTKAFETVENVLKVHDEFPCQQLYQAFA +ILVLAKFNEEGLDKFRHAVESKHADRRFVGRSYASSFLFLLSIFTVWKM +>DECOY_230 +YAHNAIYLSQAAAGGDEGSGEYKGQAALGNVEARKIFEETAAGANDRQGRWANLASAQLARGYSFTLAWPRPLPCRNIAN +LNFSAEEESQGGSLFTVGPVAPPVTRRLATVTAMAIEEPTYKIPCAHGPTVMNPKLLTGELYVHHDSLAKYVAALVKETV +YQCRKLDHDGDPLIEPEVIPVIGNQQCISAYRALVNANELIALASPTRESIKLVCRWKAFDAGDKKYQACRESLGDLGQT +TTEGDTGALPVVGKDVKIGVVIGKDQITRVFPVGNDDKQYLTEHFFIVGGICKKVRDDASFLVQRYLRRNEETNEVGIQS +LRKAMSGVSEDAALIGKGPAVIRLAIDSLEKKQEASLAPYSHPM +>DECOY_231 +FEEHFPYDKHSTCSLLACVRWNRNYSLLTTMDQSSLEFDFVKFNEAIREPTVSKPIVVLNRQMPFRILVQATTKNHKAAI +AKIRPDELLSPDEPKAWPRDPSGLPSYATVVIGKSQCYQILKEQTLYPHCEIQNVAPKYKLGPKNLIMEVQLHNFNSIGI +AKVLGEDVLEEMAAWTDLINTDSPVVNGSEDLPFFEKGPKFGTPWHILYLDLYDLKLDSLTKQCAGKVLGKEHYTCWLKS +VIFLEERKVVQERLKEQIAVGVENENQYVHACDIHRYGVDIAVKVAETVQGPPSKWTGLGLIPMKAGNNLLLRSAM +>DECOY_242 +ISISNEILVPDLYYYPIPLCKNRQRIDHSIQNLRQRFAEISRRPAEEVFHIDPFHGLPRRDDPERSLTWLVLLTICTTKV +DPLTDMFTELTTLGKTQIPPNRMSAPFNPMWATFEMQGTNVAAHKASCTYIVITVYRILEPVTRLCRPFGSSERGLLCEK +FIEQVWSQLEPDGEVAADSPYYYTIIETVYKELANWVALSDDRYYYGPLDQVGREVFDNPLYLSDYTLESLARVMVGAFG +EVGLSMGKASLGGENLLVARGISNIQVTYRTHPILLKYLPHCMPLNRLLALCFAEAILHTELLHAIAEHSYFEAYRVWTK +ALLWDWESDSPLFIPCDPGPTQSLQIAIPMMKGEPGFHLLCLPACHHQKRGSLEVTPIGEMIRYDALYINGKELEAQLCT +GEGLFPAVMDDTVPFKDPIRTCRRILGPNVGNLYQYGFFTDEAWHEAVYESVVSKKGPFIKRIDKLRKWSHKCDLLGRVK +FALAMPGLRVFFSATKLFSYRLNLNLFKTAKFNILIPFGPIYGNWEPRNPNRHRRVPPRYSPIHVYSPLGPLFVRWHYFD +QKARIEEKRHELLVPLSDDATTKGTAERLALTEYGDMWQYAPFHYIRGNPACIQVYNCYWPDKPFFAYREKHLRIIILEG +LDQPCQVTYQGVAGTAFDRGFHNLLQKHSEGQTGVITLSISDRTGSLLDTGTAVRVKYTAM
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool.conf Mon Feb 12 13:40:23 2018 -0500 @@ -0,0 +1,160 @@ +<?xml version='1.0' encoding='UTF-8'?> +<toolbox> + <section id="section-id-Peptidepropertyprediction" name="Peptide property prediction"> + <tool file="openms/PTModel.xml"/> + <tool file="openms/PTPredict.xml"/> + <tool file="openms/RTModel.xml"/> + <tool file="openms/RTPredict.xml"/> + </section> + <section id="section-id-TargetedExperiments" name="Targeted Experiments"> + <tool file="openms/InclusionExclusionListCreator.xml"/> + <tool file="openms/MRMMapper.xml"/> + <tool file="openms/OpenSwathAnalyzer.xml"/> + <tool file="openms/OpenSwathAssayGenerator.xml"/> + <tool file="openms/OpenSwathChromatogramExtractor.xml"/> + <tool file="openms/OpenSwathConfidenceScoring.xml"/> + <tool file="openms/OpenSwathDecoyGenerator.xml"/> + <tool file="openms/OpenSwathDIAPreScoring.xml"/> + <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/> + <tool file="openms/OpenSwathFileSplitter.xml"/> + <tool file="openms/OpenSwathMzMLFileCacher.xml"/> + <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/> + <tool file="openms/OpenSwathRTNormalizer.xml"/> + <tool file="openms/PrecursorIonSelector.xml"/> + <tool file="openms/TargetedFileConverter.xml"/> + </section> + <section id="section-id-Utilities" name="Utilities"> + <tool file="openms/AccurateMassSearch.xml"/> + <tool file="openms/CVInspector.xml"/> + <tool file="openms/DatabaseFilter.xml"/> + <tool file="openms/DecoyDatabase.xml"/> + <tool file="openms/DeMeanderize.xml"/> + <tool file="openms/Digestor.xml"/> + <tool file="openms/DigestorMotif.xml"/> + <tool file="openms/ERPairFinder.xml"/> + <tool file="openms/FFEval.xml"/> + <tool file="openms/FuzzyDiff.xml"/> + <tool file="openms/IDDecoyProbability.xml"/> + <tool file="openms/IDExtractor.xml"/> + <tool file="openms/IDMassAccuracy.xml"/> + <tool file="openms/IDScoreSwitcher.xml"/> + <tool file="openms/IDSplitter.xml"/> + <tool file="openms/LabeledEval.xml"/> + <tool file="openms/LowMemPeakPickerHiRes.xml"/> + <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/> + <tool file="openms/MassCalculator.xml"/> + <tool file="openms/MetaboliteSpectralMatcher.xml"/> + <tool file="openms/MetaProSIP.xml"/> + <tool file="openms/MRMPairFinder.xml"/> + <tool file="openms/MRMTransitionGroupPicker.xml"/> + <tool file="openms/MSSimulator.xml"/> + <tool file="openms/MultiplexResolver.xml"/> + <tool file="openms/MzMLSplitter.xml"/> + <tool file="openms/OpenSwathWorkflow.xml"/> + <tool file="openms/QCCalculator.xml"/> + <tool file="openms/QCEmbedder.xml"/> + <tool file="openms/QCExporter.xml"/> + <tool file="openms/QCExtractor.xml"/> + <tool file="openms/QCImporter.xml"/> + <tool file="openms/QCMerger.xml"/> + <tool file="openms/QCShrinker.xml"/> + <tool file="openms/RNPxl.xml"/> + <tool file="openms/RNPxlSearch.xml"/> + <tool file="openms/RNPxlXICFilter.xml"/> + <tool file="openms/RTEvaluation.xml"/> + <tool file="openms/SemanticValidator.xml"/> + <tool file="openms/SequenceCoverageCalculator.xml"/> + <tool file="openms/SimpleSearchEngine.xml"/> + <tool file="openms/SpecLibCreator.xml"/> + <tool file="openms/SpectraSTSearchAdapter.xml"/> + <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/> + <tool file="openms/TICCalculator.xml"/> + <tool file="openms/TopPerc.xml"/> + <tool file="openms/TransformationEvaluation.xml"/> + <tool file="openms/XMLValidator.xml"/> + </section> + <section id="section-id-MapAlignment" name="Map Alignment"> + <tool file="openms/ConsensusMapNormalizer.xml"/> + <tool file="openms/FeatureLinkerLabeled.xml"/> + <tool file="openms/FeatureLinkerUnlabeled.xml"/> + <tool file="openms/FeatureLinkerUnlabeledKD.xml"/> + <tool file="openms/FeatureLinkerUnlabeledQT.xml"/> + <tool file="openms/MapRTTransformer.xml"/> + </section> + <section id="section-id-IDProcessing" name="ID Processing"> + <tool file="openms/ConsensusID.xml"/> + <tool file="openms/FalseDiscoveryRate.xml"/> + <tool file="openms/FidoAdapter.xml"/> + <tool file="openms/IDConflictResolver.xml"/> + <tool file="openms/IDFileConverter.xml"/> + <tool file="openms/IDFilter.xml"/> + <tool file="openms/IDMapper.xml"/> + <tool file="openms/IDPosteriorErrorProbability.xml"/> + <tool file="openms/IDRTCalibration.xml"/> + <tool file="openms/LuciphorAdapter.xml"/> + <tool file="openms/PeptideIndexer.xml"/> + <tool file="openms/PhosphoScoring.xml"/> + </section> + <section id="section-id-Signalprocessingandpreprocessing" name="Signal processing and preprocessing"> + <tool file="openms/BaselineFilter.xml"/> + <tool file="openms/ExternalCalibration.xml"/> + <tool file="openms/HighResPrecursorMassCorrector.xml"/> + <tool file="openms/InternalCalibration.xml"/> + <tool file="openms/MapNormalizer.xml"/> + <tool file="openms/MassTraceExtractor.xml"/> + <tool file="openms/NoiseFilterGaussian.xml"/> + <tool file="openms/NoiseFilterSGolay.xml"/> + <tool file="openms/PeakPickerHiRes.xml"/> + <tool file="openms/PeakPickerIterative.xml"/> + <tool file="openms/PeakPickerWavelet.xml"/> + <tool file="openms/PrecursorMassCorrector.xml"/> + <tool file="openms/SpectraMerger.xml"/> + <tool file="openms/TOFCalibration.xml"/> + </section> + <section id="section-id-Identification" name="Identification"> + <tool file="openms/CompNovoCID.xml"/> + <tool file="openms/CompNovo.xml"/> + <tool file="openms/InspectAdapter.xml"/> + <tool file="openms/MascotAdapter.xml"/> + <tool file="openms/MascotAdapterOnline.xml"/> + <tool file="openms/MSGFPlusAdapter.xml"/> + <tool file="openms/ProteinInference.xml"/> + <tool file="openms/SpectraFilterBernNorm.xml"/> + <tool file="openms/SpectraFilterMarkerMower.xml"/> + <tool file="openms/SpectraFilterNLargest.xml"/> + <tool file="openms/SpectraFilterNormalizer.xml"/> + <tool file="openms/SpectraFilterParentPeakMower.xml"/> + <tool file="openms/SpectraFilterScaler.xml"/> + <tool file="openms/SpectraFilterSqrtMower.xml"/> + <tool file="openms/SpectraFilterThresholdMower.xml"/> + <tool file="openms/SpectraFilterWindowMower.xml"/> + <tool file="openms/XTandemAdapter.xml"/> + </section> + <section id="section-id-FileHandling" name="File Handling"> + <tool file="openms/DTAExtractor.xml"/> + <tool file="openms/FileConverter.xml"/> + <tool file="openms/FileFilter.xml"/> + <tool file="openms/FileInfo.xml"/> + <tool file="openms/FileMerger.xml"/> + <tool file="openms/IDMerger.xml"/> + <tool file="openms/IDRipper.xml"/> + <tool file="openms/MapStatistics.xml"/> + <tool file="openms/MzTabExporter.xml"/> + <tool file="openms/TextExporter.xml"/> + </section> + <section id="section-id-Quantitation" name="Quantitation"> + <tool file="openms/AdditiveSeries.xml"/> + <tool file="openms/Decharger.xml"/> + <tool file="openms/EICExtractor.xml"/> + <tool file="openms/FeatureFinderCentroided.xml"/> + <tool file="openms/FeatureFinderIdentification.xml"/> + <tool file="openms/FeatureFinderIsotopeWavelet.xml"/> + <tool file="openms/FeatureFinderMetabo.xml"/> + <tool file="openms/FeatureFinderMRM.xml"/> + <tool file="openms/FeatureFinderMultiplex.xml"/> + <tool file="openms/FeatureFinderSuperHirn.xml"/> + <tool file="openms/IsobaricAnalyzer.xml"/> + <tool file="openms/ProteinQuantifier.xml"/> + <tool file="openms/ProteinResolver.xml"/> + </section> +</toolbox>