| Next changeset 1:79186fbde4ea (2017-04-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 |
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added:
IDMapper.xml SKIP_TOOLS_FILE.txt datatypes_conf.xml filetypes.txt macros.xml readme.md repository_dependencies.xml test-data/DecoyDatabase_input.fasta test-data/DecoyDatabase_output.fasta tool.conf |
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| diff -r 000000000000 -r 026dbe52de09 IDMapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/IDMapper.xml Wed Mar 01 12:31:09 2017 -0500 |
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| @@ -0,0 +1,86 @@ +<?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 CTD2Galaxy.--> +<!--Proposed Tool Section: [ID Processing]--> +<tool id="IDMapper" name="IDMapper" version="2.1.0"> + <description>Assigns protein/peptide identifications to features or consensus features.</description> + <macros> + <token name="@EXECUTABLE@">IDMapper</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>IDMapper + +#if $param_id: + -id $param_id +#end if +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_rt_tolerance: + -rt_tolerance $param_rt_tolerance +#end if +#if $param_mz_tolerance: + -mz_tolerance $param_mz_tolerance +#end if +#if $param_mz_measure: + -mz_measure $param_mz_measure +#end if +#if $param_mz_reference: + -mz_reference $param_mz_reference +#end if +#if $param_ignore_charge: + -ignore_charge +#end if +#if $param_feature_use_centroid_rt: + -feature:use_centroid_rt +#end if +#if $param_feature_use_centroid_mz: + -feature:use_centroid_mz +#end if +#if $param_consensus_use_subelements: + -consensus:use_subelements +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_consensus_annotate_ids_with_subelements: + -consensus:annotate_ids_with_subelements +#end if +#end if +</command> + <inputs> + <param name="param_id" type="data" format="mzid,idxml" optional="False" label="Protein/peptide identifications file" help="(-id) "/> + <param name="param_in" type="data" format="featurexml,consensusxml,mzq" optional="False" label="Feature map/consensus map file" help="(-in) "/> + <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="(-rt_tolerance) <br>Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/> + <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="(-mz_tolerance) <br>Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/> + <param name="param_mz_measure" display="radio" type="select" optional="False" value="ppm" label="Unit of 'mz_tolerance'" help="(-mz_measure) "> + <option value="ppm" selected="true">ppm</option> + <option value="Da">Da</option> + </param> + <param name="param_mz_reference" display="radio" type="select" optional="False" value="precursor" label="Source of m/z values for peptide identifications" help="(-mz_reference) If 'precursor', the precursor-m/z from the idXML is used. If 'peptide', <br>masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches. <br>('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)"> + <option value="precursor" selected="true">precursor</option> + <option value="peptide">peptide</option> + </param> + <param name="param_ignore_charge" display="radio" type="boolean" truevalue="-ignore_charge" falsevalue="" checked="false" optional="True" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" help="(-ignore_charge) "/> + <param name="param_feature_use_centroid_rt" display="radio" type="boolean" truevalue="-feature:use_centroid_rt" falsevalue="" checked="false" optional="True" label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces" help="(-use_centroid_rt) "/> + <param name="param_feature_use_centroid_mz" display="radio" type="boolean" truevalue="-feature:use_centroid_mz" falsevalue="" checked="false" optional="True" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces" help="(-use_centroid_mz) <br>(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)"/> + <param name="param_consensus_use_subelements" display="radio" type="boolean" truevalue="-consensus:use_subelements" falsevalue="" checked="false" optional="True" label="Match using RT and m/z of sub-features instead of consensus RT and m/z" help="(-use_subelements) A consensus feature matches if any of its sub-features matches"/> + <expand macro="advanced_options"> + <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <param name="param_consensus_annotate_ids_with_subelements" display="radio" type="boolean" truevalue="-consensus:annotate_ids_with_subelements" falsevalue="" checked="false" optional="True" label="Store the map index of the sub-feature in the peptide ID" help="(-annotate_ids_with_subelements) "/> + </expand> + </inputs> + <outputs> + <data name="param_out" metadata_source="param_in" format="input"/> + </outputs> + <help>Assigns protein/peptide identifications to features or consensus features. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html</help> +</tool> |
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| diff -r 000000000000 -r 026dbe52de09 SKIP_TOOLS_FILE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SKIP_TOOLS_FILE.txt Wed Mar 01 12:31:09 2017 -0500 |
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| @@ -0,0 +1,9 @@ +OMSSAAdapter +MyriMatchAdapter +PepNovoAdapter +SeedListGenerator +SpecLibSearcher +MapAlignerIdentification +MapAlignerPoseClustering +MapAlignerSpectrum +MapAlignerRTTransformer |
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| diff -r 000000000000 -r 026dbe52de09 datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Wed Mar 01 12:31:09 2017 -0500 |
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| @@ -0,0 +1,33 @@ +<?xml version='1.0' encoding='UTF-8'?> +<datatypes> + <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> + <datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml"/> + <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/> + <datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXM" mimetype="application/xml"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text"/> + <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/> + <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf"/> + <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml"/> + <datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/> + <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/> + <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp"/> + <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/> + <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/> + <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml"/> + <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/> + <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml"/> + <datatype extension="grid" type="galaxy.datatypes.data:Grid"/> + <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml"/> + <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/> + <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/> + <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml"/> + <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text"/> + <datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text"/> + </registration> +</datatypes> |
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| diff -r 000000000000 -r 026dbe52de09 filetypes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filetypes.txt Wed Mar 01 12:31:09 2017 -0500 |
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| @@ -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:IdXM 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 \ No newline at end of file |
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| diff -r 000000000000 -r 026dbe52de09 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Mar 01 12:31:09 2017 -0500 |
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| @@ -0,0 +1,35 @@ +<?xml version='1.0' encoding='UTF-8'?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.1">openms</requirement> + <requirement type="package" version="15.12.15.2">xtandem</requirement> + <requirement type="package" version="1.0">fido</requirement> + <requirement type="package" version="2016.10.26">msgf_plus</requirement> + </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> |
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| diff -r 000000000000 -r 026dbe52de09 readme.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.md Wed Mar 01 12:31:09 2017 -0500 |
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| @@ -0,0 +1,165 @@ +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 the Tool Shed) + * create a folder called CTD + * inside of your new installed openms/bin folder, execute the following command: + + ```bash + for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; + ``` + + * `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/blankclemens/CTD2Galaxy.git + ``` + + * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. + + ```bash + python generator.py \ + -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_executable \ + xtandem_executable param_model_directory \ + java_executable java_memory java_permgen \ + -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ + -s PATH/TO/SKIP_TOOLS_FILES.txt + ``` + + + * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: + + ``` + sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml + sed -i '13 a\-fidocp_executable fido_choose_parameters' 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 `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line + + -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit + + and change it to + + -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit" + + * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: + + <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> + ``` + + + * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in Galaxy-stable and are therefore in `SKIP_TOOLS_FILES.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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| diff -r 000000000000 -r 026dbe52de09 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Wed Mar 01 12:31:09 2017 -0500 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Required proteomics dependencies."> + <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 000000000000 -r 026dbe52de09 test-data/DecoyDatabase_input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DecoyDatabase_input.fasta Wed Mar 01 12:31:09 2017 -0500 |
| b |
| b'@@ -0,0 +1,146 @@\n+>12 \n+MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI\n+STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL\n+YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM\n+VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR\n+DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL\n+MIIVPTDTQNIFFMSKVTNPKQA\n+>18\n+MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMK\n+QLNIIQNAEAVHFFCNYEESRGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQ\n+NASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLITMACGSCSNENALKTIFMWYR\n+SKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS\n+FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGG\n+DNHASDDFFRKLRDIARKHGCAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMM\n+TGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIKREDLLNNAAHAGKALLTGLL\n+DLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF\n+RDHHAHLFLNIFSDILADFK\n+>88\n+MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIE\n+NIEEDFRNGLKLMLLLEVISGERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAE\n+EIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNIQNFHTSW\n+KDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP\n+DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRT\n+IPWLENRTPEKTMQAMQKKLEDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAF\n+MPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLEHLAEKFRQKASTHETWAYGK\n+EQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN\n+DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQ\n+DMFIVHSIEEIQSLITAHEQFKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYS\n+TVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRRQFAAQANAIGPWIQNKMEEI\n+ARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI\n+RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRA\n+CLISMGYDLGEAEFARIMTLVDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILAS\n+DKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALDYAAFSSALYGESDL\n+>112\n+MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGP\n+PRCPWQDDAFIRRGGPGKGKELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWR\n+RLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLVLLTAVLLAFHAAPARPQPAY\n+VALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW\n+CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTN\n+VIGICTHYPAEVSQRQAFQETRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINT\n+KKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHC\n+LRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV\n+HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNA\n+YLKEQHIETFLILGASQKRKEEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFR\n+QMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQLRKDHVRRFLLTFQREDLEKK\n+YSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC\n+GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLT\n+PADITACHLQQLNYSLGLDAPLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLA\n+MIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNETFDGLDCPAAGRVALKYMTPV\n+ILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF\n+LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIIS\n+EERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNN\n+FQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVLAAKG\n+YQLECRGVVKVKGKGEMTTYFLNGGPSS\n+>114\n+MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGS\n+GSGGSGKASDPAGGGPNHHAPQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASG\n+SGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNSFKSRDLERLYQRYFLGQRRK\n+SEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT\n+YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTS\n+LLQVILQVVIPRLAVISINQVVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEAR\n+LRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQHQFHRIYIHRYENVSILFADV\n+KGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH\n+CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKL\n+ESGGIPGRIHISKATLDCLNGDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPED\n+IVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLAALTRNSINLLPNHLAQALHV\n+QSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF\n+IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINE\n+TYLARNVIIFASILINFLGAILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTG\n'..b'VPEETYLIL\n+KDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV\n+QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP\n+>143\n+MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQ\n+LNSIQKNHVHIANPDFIWKSIREKRLLDVKNYDPYKPLDITPPPDQKASSSEVKTEGLCP\n+DSATEEEDTVELTEFGMQNVEIPHLPQDFEVAKYNTLEKVGMEGGQEAVVVELQCSRDSR\n+DCPFLISSHFLLDDGMETRRQFAIKKTSEDASEYFENYIEELKKQGFLLREHFTPEATQL\n+ASEQLQALLLEEVMNSSTLSQEVSDLVEMIWAEALGHLEHMLLKPVNRISLNDVSKAEGI\n+LLLVKAALKNGETAEQLQKMMTEFYRLIPHKGTMPKEVNLGLLAKKADLCQLIRDMVNVC\n+ETNLSKPNPPSLAKYRALRCKIEHVEQNTEEFLRVRKEVLQNHHSKSPVDVLQIFRVGRV\n+NETTEFLSKLGNVRPLLHGSPVQNIVGILCRGLLLPKVVEDRGVQRTDVGNLGSGIYFSD\n+SLSTSIKYSHPGETDGTRLLLICDVALGKCMDLHEKDFSLTEAPPGYDSVHGVSQTASVT\n+TDFEDDEFVVYKTNQVKMKYIIKFSMPGDQIKDFHPSDHTELEEYRPEFSNFSKVEDYQL\n+PDAKTSSSTKAGLQDASGNLVPLEDVHIKGRIIDTVAQVIVFQTYTNKSHVPIEAKYIFP\n+LDDKAAVCGFEAFINGKHIVGEIKEKEEAQQEYLEAVTQGHGAYLMSQDAPDVFTVSVGN\n+LPPKAKVLIKITYITELSILGTVGVFFMPATVAPWQQDKALNENLQDTVEKICIKEIGTK\n+QSFSLTMSIEMPYVIEFIFSDTHELKQKRTDCKAVISTMEGSSLDSSGFSLHIGLSAAYL\n+PRMWVEKHPEKESEACMLVFQPDLDVDLPDLASESEVIICLDCSSSMEGVTFLQAKQIAL\n+HALSLVGEKQKVNIIQFGTGYKELFSYPKHITSNTMAAEFIMSATPTMGNTDFWKTLRYL\n+SLLYPARGSRNILLVSDGHLQDESLTLQLVKRSRPHTRLFACGIGSTANRHVLRILSQCG\n+AGVFEYFNAKSKHSWRKQIEDQMTRLCSPSCHSVSVKWQQLNPDVPEALQAPAQVPSLFL\n+NDRLLVYGFIPHCTQATLCALIQEKEFRTMVSTTELQKTTGTMIHKLAARALIRDYEDGI\n+LHENETSHEMKKQTLKSLIIKLSKENSLITQFTSFVAVEKRDENESPFPDIPKVSELIAK\n+EDVDFLPYMSWQGEPQEAVRNQSLLASSEWPELRLSKRKHRKIPFSKRKMELSQPEVSED\n+FEEDGLGVLPAFTSNLERGGVEKLLDLSWTESCKPTATEPLFKKVSPWETSTSSFFPILA\n+PAVGSYLPPTARAHSPASLSFASYRQVASFGSAAPPRQFDASQFSQGPVPGTCADWIPQS\n+ASCPTGPPQNPPSSPYCGIVFSGSSLSSAQSAPLQHPGGFTTRPSAGTFPELDSPQLHFS\n+LPTDPDPIRGFGSYHPSASSPFHFQPSAASLTANLRLPMASALPEALCSQSRTTPVDLCL\n+LEESVGSLEGSRCPVFAFQSSDTESDELSEVLQDSCFLQIKCDTKDDSILCFLEVKEEDE\n+IVCIQHWQDAVPWTELLSLQTEDGFWKLTPELGLILNLNTNGLHSFLKQKGIQSLGVKGR\n+ECLLDLIATMLVLQFIRTRLEKEGIVFKSLMKMDDASISRNIPWAFEAIKQASEWVRRTE\n+GQYPSICPRLELGNDWDSATKQLLGLQPISTVSPLHRVLHYSQG\n+>213\n+MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF\n+EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP\n+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF\n+FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV\n+ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK\n+ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR\n+RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE\n+QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV\n+LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL\n+SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV\n+AASQAALGL\n+>230\n+MPHSYPALSAEQKKELSDIALRIVAPGKGILAADESVGSMAKRLSQIGVENTEENRRLYR\n+QVLFSADDRVKKCIGGVIFFHETLYQKDDNGVPFVRTIQDKGIVVGIKVDKGVVPLAGTD\n+GETTTQGLDGLSERCAQYKKDGADFAKWRCVLKISERTPSALAILENANVLARYASICQQ\n+NGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHVYLEGTLLKPNMVTPGHAC\n+PIKYTPEEIAMATVTALRRTVPPAVPGVTFLSGGQSEEEASFNLNAINRCPLPRPWALTF\n+SYGRALQASALNAWRGQRDNAGAATEEFIKRAEVNGLAAQGKYEGSGEDGGAAAQSLYIA\n+NHAY\n+>231\n+MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQ\n+EKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGK\n+EFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKP\n+AVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAK\n+HNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCA\n+LLSCTSHKDYPFHEEF\n+>242\n+MATYKVRVATGTDLLSGTRDSISLTIVGTQGESHKQLLNHFGRDFATGAVGQYTVQCPQD\n+LGELIIIRLHKERYAFFPKDPWYCNYVQICAPNGRIYHFPAYQWMDGYETLALREATGKT\n+TADDSLPVLLEHRKEEIRAKQDFYHWRVFLPGLPSYVHIPSYRPPVRRHRNPNRPEWNGY\n+IPGFPILINFKATKFLNLNLRYSFLKTASFFVRLGPMALAFKVRGLLDCKHSWKRLKDIR\n+KIFPGKKSVVSEYVAEHWAEDTFFGYQYLNGVNPGLIRRCTRIPDKFPVTDDMVAPFLGE\n+GTCLQAELEKGNIYLADYRIMEGIPTVELSGRKQHHCAPLCLLHFGPEGKMMPIAIQLSQ\n+TPGPDCPIFLPSDSEWDWLLAKTWVRYAEFYSHEAIAHLLETHLIAEAFCLALLRNLPMC\n+HPLYKLLIPHTRYTVQINSIGRAVLLNEGGLSAKGMSLGVEGFAGVMVRALSELTYDSLY\n+LPNDFVERGVQDLPGYYYRDDSLAVWNALEKYVTEIITYYYPSDAAVEGDPELQSWVQEI\n+FKECLLGRESSGFPRCLRTVPELIRYVTIVIYTCSAKHAAVNTGQMEFTAWMPNFPASMR\n+NPPIQTKGLTTLETFMDTLPDVKTTCITLLVLWTLSREPDDRRPLGHFPDIHFVEEAPRR\n+SIEAFRQRLNQISHDIRQRNKCLPIPYYYLDPVLIENSISI\n' |
| b |
| diff -r 000000000000 -r 026dbe52de09 test-data/DecoyDatabase_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DecoyDatabase_output.fasta Wed Mar 01 12:31:09 2017 -0500 |
| b |
| b'@@ -0,0 +1,228 @@\n+>12 \n+MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI\n+STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL\n+YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM\n+VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR\n+DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL\n+MIIVPTDTQNIFFMSKVTNPKQA\n+>18 \n+MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMKQLNIIQNAEAVHFFCNYEES\n+RGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQNASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLIT\n+MACGSCSNENALKTIFMWYRSKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS\n+FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGGDNHASDDFFRKLRDIARKHG\n+CAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMMTGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIK\n+REDLLNNAAHAGKALLTGLLDLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF\n+RDHHAHLFLNIFSDILADFK\n+>88 \n+MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVIS\n+GERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLW\n+CQRKTAPYRNVNIQNFHTSWKDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP\n+DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRTIPWLENRTPEKTMQAMQKKL\n+EDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAFMPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLE\n+HLAEKFRQKASTHETWAYGKEQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN\n+DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQDMFIVHSIEEIQSLITAHEQ\n+FKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYSTVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRR\n+QFAAQANAIGPWIQNKMEEIARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI\n+RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRACLISMGYDLGEAEFARIMTL\n+VDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILASDKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALD\n+YAAFSSALYGESDL\n+>112 \n+MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGPPRCPWQDDAFIRRGGPGKGK\n+ELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWRRLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLV\n+LLTAVLLAFHAAPARPQPAYVALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW\n+CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTNVIGICTHYPAEVSQRQAFQE\n+TRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINTKKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQEL\n+VMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV\n+HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNAYLKEQHIETFLILGASQKRK\n+EEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFRQMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQL\n+RKDHVRRFLLTFQREDLEKKYSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC\n+GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLTPADITACHLQQLNYSLGLDA\n+PLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLAMIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNET\n+FDGLDCPAAGRVALKYMTPVILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF\n+LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAA\n+SGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDST\n+GVPDRIQVTTDLYQVLAAKGYQLECRGVVKVKGKGEMTTYFLNGGPSS\n+>114 \n+MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGSGSGGSGKASDPAGGGPNHHA\n+PQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASGSGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNS\n+FKSRDLERLYQRYFLGQRRKSEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT\n+YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTSLLQVILQVVIPRLAVISINQ\n+VVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEARLRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQH\n+QFHRIYIHRYENVSILFADVKGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH\n+CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKLESGGIPGRIHISKATLDCLN\n+GDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPEDIVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLA\n+ALTRNSINLLPNHLAQALHVQSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF\n+IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINETYLARNVIIFASILINFLGA\n+ILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTGVLAMVTCAVFLRLNSVLKLAVLL'..b'SGSASGSGSREPFVKTGCTSHAREGPGLSYLPLASDGSLQPAHHNPGGGAPDSAKGSGGSGSGSGGRHGH\n+IFRQETIHRVATQWLLRQPRSASRGDGAPPTPHITYLEESGTLCRVDSLEM\n+>DECOY_143 \n+GQSYHLVRHLPSVTSIPQLGLLQKTASDWDNGLELRPCISPYQGETRRVWESAQKIAEFAWPINRSISADDMKMLSKFVI\n+GEKELRTRIFQLVLMTAILDLLCERGKVGLSQIGKQKLFSHLGNTNLNLILGLEPTLKWFGDETQLSLLETWPVADQWHQ\n+ICVIEDEEKVELFCLISDDKTDCKIQLFCSDQLVESLEDSETDSSQFAFVPCRSGELSGVSEELLCLDVPTTRSQSCLAE\n+PLASAMPLRLNATLSAASPQFHFPSSASPHYSGFGRIPDPDTPLSFHLQPSDLEPFTGASPRTTFGGPHQLPASQASSLS\n+SGSFVIGCYPSSPPNQPPGTPCSASQPIWDACTGPVPGQSFQSADFQRPPAASGFSAVQRYSAFSLSAPSHARATPPLYS\n+GVAPALIPFFSSTSTEWPSVKKFLPETATPKCSETWSLDLLKEVGGRELNSTFAPLVGLGDEEFDESVEPQSLEMKRKSF\n+PIKRHKRKSLRLEPWESSALLSQNRVAEQPEGQWSMYPLFDVDEKAILESVKPIDPFPSENEDRKEVAVFSTFQTILSNE\n+KSLKIILSKLTQKKMEHSTENEHLIGDEYDRILARAALKHIMTGTTKQLETTSVMTRFEKEQILACLTAQTCHPIFGYVL\n+LRDNLFLSPVQAPAQLAEPVDPNLQQWKVSVSHCSPSCLRTMQDEIQKRWSHKSKANFYEFVGAGCQSLIRLVHRNATSG\n+IGCAFLRTHPRSRKVLQLTLSEDQLHGDSVLLINRSGRAPYLLSLYRLTKWFDTNGMTPTASMIFEAAMTNSTIHKPYSF\n+LEKYGTGFQIINVKQKEGVLSLAHLAIQKAQLFTVGEMSSSCDLCIIVESESALDPLDVDLDPQFVLMCAESEKEPHKEV\n+WMRPLYAASLGIHLSFGSSDLSSGEMTSIVAKCDTRKQKLEHTDSFIFEIVYPMEISMTLSFSQKTGIEKICIKEVTDQL\n+NENLAKDQQWPAVTAPMFFVGVTGLISLETIYTIKILVKAKPPLNGVSVTFVDPADQSMLYAGHGQTVAELYEQQAEEKE\n+KIEGVIHKGNIFAEFGCVAAKDDLPFIYKAEIPVHSKNTYTQFVIVQAVTDIIRGKIHVDELPVLNGSADQLGAKTSSST\n+KADPLQYDEVKSFNSFEPRYEELETHDSPHFDKIQDGPMSFKIIYKMKVQNTKYVVFEDDEFDTTVSATQSVGHVSDYGP\n+PAETLSFDKEHLDMCKGLAVDCILLLRTGDTEGPHSYKISTSLSDSFYIGSGLNGVDTRQVGRDEVVKPLLLGRCLIGVI\n+NQVPSGHLLPRVNGLKSLFETTENVRGVRFIQLVDVPSKSHHNQLVEKRVRLFEETNQEVHEIKCRLARYKALSPPNPKS\n+LNTECVNVMDRILQCLDAKKALLGLNVEKPMTGKHPILRYFETMMKQLQEATEGNKLAAKVLLLIGEAKSVDNLSIRNVP\n+KLLMHELHGLAEAWIMEVLDSVEQSLTSSNMVEELLLAQLQESALQTAEPTFHERLLFGQKKLEEIYNEFYESADESTKK\n+IAFQRRTEMGDDLLFHSSILFPCDRSDRSCQLEVVVAEQGGEMGVKELTNYKAVEFDQPLHPIEVNQMGFETLEVTDEEE\n+TASDPCLGETKVESSSAKQDPPPTIDLPKYPDYNKVDLLRKERISKWIFDPNAIHVHNKQISNLQYQSLVDANDLIIHTC\n+QPNLSFSFKGGNEKIDTQLKKKQQQPLYKVKLCFICNAFIGMVM\n+>DECOY_213 \n+LGLAAQSAAVLKKGEEAFCTEKDDAKCCKEVFAAFDDMVAKLQEKTAKPKHKVLEVLATQKKIQREKESLTCIDAHFTFT\n+EANFEKPVYTEDVELASFCPRRNVLSETCCKTVRDSVPTKEHLVCLQNLVVSLYDEACPMRKAEPHKCCKSGVKGLNRSV\n+EVLTPTSVQPVKKTYRVLLANQFKYEGLQEFLECNQKILNQPEEVLPKFEDFVKAYCEHPDAAACCKELTTEYTKALRLL\n+LVVSYDPHRRAYEYLFMGLFVDKAEAYNKCVDKSEVFDAALSPLDAPMEDNEVEAICHSKELLPKECCEKLKSSISDQNE\n+CIYKALDARDDACELLDGHCCETHVKTLDTVLKSVEAFEAKPFRQSLRAVAWAKFAREGFKQLSACKLRQKASSAKGEDR\n+LEDLKPLLCAAKDAAQCCETFAAKYRKAFFLLEPAYFYPHRRAIEYLYKKLFTEENDHFATCMVDVEPRVLRPLNPNDDK\n+HQLFCENREPEQKACCDAMEGYTERLTAVTCLKDGFLTHLSKDCNEASEDAVCTKAFETVENVLKVHDEFPCQQLYQAFA\n+ILVLAKFNEEGLDKFRHAVESKHADRRFVGRSYASSFLFLLSIFTVWKM\n+>DECOY_230 \n+YAHNAIYLSQAAAGGDEGSGEYKGQAALGNVEARKIFEETAAGANDRQGRWANLASAQLARGYSFTLAWPRPLPCRNIAN\n+LNFSAEEESQGGSLFTVGPVAPPVTRRLATVTAMAIEEPTYKIPCAHGPTVMNPKLLTGELYVHHDSLAKYVAALVKETV\n+YQCRKLDHDGDPLIEPEVIPVIGNQQCISAYRALVNANELIALASPTRESIKLVCRWKAFDAGDKKYQACRESLGDLGQT\n+TTEGDTGALPVVGKDVKIGVVIGKDQITRVFPVGNDDKQYLTEHFFIVGGICKKVRDDASFLVQRYLRRNEETNEVGIQS\n+LRKAMSGVSEDAALIGKGPAVIRLAIDSLEKKQEASLAPYSHPM\n+>DECOY_231 \n+FEEHFPYDKHSTCSLLACVRWNRNYSLLTTMDQSSLEFDFVKFNEAIREPTVSKPIVVLNRQMPFRILVQATTKNHKAAI\n+AKIRPDELLSPDEPKAWPRDPSGLPSYATVVIGKSQCYQILKEQTLYPHCEIQNVAPKYKLGPKNLIMEVQLHNFNSIGI\n+AKVLGEDVLEEMAAWTDLINTDSPVVNGSEDLPFFEKGPKFGTPWHILYLDLYDLKLDSLTKQCAGKVLGKEHYTCWLKS\n+VIFLEERKVVQERLKEQIAVGVENENQYVHACDIHRYGVDIAVKVAETVQGPPSKWTGLGLIPMKAGNNLLLRSAM\n+>DECOY_242 \n+ISISNEILVPDLYYYPIPLCKNRQRIDHSIQNLRQRFAEISRRPAEEVFHIDPFHGLPRRDDPERSLTWLVLLTICTTKV\n+DPLTDMFTELTTLGKTQIPPNRMSAPFNPMWATFEMQGTNVAAHKASCTYIVITVYRILEPVTRLCRPFGSSERGLLCEK\n+FIEQVWSQLEPDGEVAADSPYYYTIIETVYKELANWVALSDDRYYYGPLDQVGREVFDNPLYLSDYTLESLARVMVGAFG\n+EVGLSMGKASLGGENLLVARGISNIQVTYRTHPILLKYLPHCMPLNRLLALCFAEAILHTELLHAIAEHSYFEAYRVWTK\n+ALLWDWESDSPLFIPCDPGPTQSLQIAIPMMKGEPGFHLLCLPACHHQKRGSLEVTPIGEMIRYDALYINGKELEAQLCT\n+GEGLFPAVMDDTVPFKDPIRTCRRILGPNVGNLYQYGFFTDEAWHEAVYESVVSKKGPFIKRIDKLRKWSHKCDLLGRVK\n+FALAMPGLRVFFSATKLFSYRLNLNLFKTAKFNILIPFGPIYGNWEPRNPNRHRRVPPRYSPIHVYSPLGPLFVRWHYFD\n+QKARIEEKRHELLVPLSDDATTKGTAERLALTEYGDMWQYAPFHYIRGNPACIQVYNCYWPDKPFFAYREKHLRIIILEG\n+LDQPCQVTYQGVAGTAFDRGFHNLLQKHSEGQTGVITLSISDRTGSLLDTGTAVRVKYTAM\n' |
| b |
| diff -r 000000000000 -r 026dbe52de09 tool.conf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool.conf Wed Mar 01 12:31:09 2017 -0500 |
| b |
| @@ -0,0 +1,162 @@ +<?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-DEFAULT" name="DEFAULT"> + <tool file="openms/OpenSwathFileSplitter.xml"/> + <tool file="openms/OpenSwathMzMLFileCacher.xml"/> + </section> + <section id="section-id-TargetedExperiments" name="Targeted Experiments"> + <tool file="openms/ConvertTraMLToTSV.xml"/> + <tool file="openms/ConvertTSVToTraML.xml"/> + <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/OpenSwathRewriteToFeatureXML.xml"/> + <tool file="openms/OpenSwathRTNormalizer.xml"/> + <tool file="openms/PrecursorIonSelector.xml"/> + </section> + <section id="section-id-Utilities" name="Utilities"> + <tool file="openms/AccurateMassSearch.xml"/> + <tool file="openms/CVInspector.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/MapAlignmentEvaluation.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/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/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/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/ITRAQAnalyzer.xml"/> + <tool file="openms/ProteinQuantifier.xml"/> + <tool file="openms/ProteinResolver.xml"/> + <tool file="openms/TMTAnalyzer.xml"/> + </section> +</toolbox> |