Repository 'openms_spectrastsearchadapter'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/openms_spectrastsearchadapter

Changeset 0:369f340978e4 (2017-08-09)
Next changeset 1:2c3ee84c962d (2017-10-18)
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
added:
SKIP_TOOLS_FILE.txt
SpectraSTSearchAdapter.xml
filetypes.txt
macros.xml
readme.md
repository_dependencies.xml
test-data/DecoyDatabase_input.fasta
test-data/DecoyDatabase_output.fasta
tool.conf
b
diff -r 000000000000 -r 369f340978e4 SKIP_TOOLS_FILE.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SKIP_TOOLS_FILE.txt Wed Aug 09 09:11:13 2017 -0400
b
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer
b
diff -r 000000000000 -r 369f340978e4 SpectraSTSearchAdapter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpectraSTSearchAdapter.xml Wed Aug 09 09:11:13 2017 -0400
[
@@ -0,0 +1,100 @@
+<?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: [Utilities]-->
+<tool id="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="2.2.0.1">
+  <description>Interface to the SEARCH Mode of the SpectraST executable</description>
+  <macros>
+    <token name="@EXECUTABLE@">SpectraSTSearchAdapter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>SpectraSTSearchAdapter
+
+-spectra_files
+  #for token in $param_spectra_files:
+    $token
+  #end for
+
+#if $rep_param_output_files:
+-output_files
+  #for token in $rep_param_output_files:
+    #if " " in str(token):
+      "$token.param_output_files"
+    #else
+      $token.param_output_files
+    #end if
+  #end for
+#end if
+#if $param_library_file:
+  -library_file $param_library_file
+#end if
+#if $param_sequence_database_file:
+  -sequence_database_file $param_sequence_database_file
+#end if
+#if $param_sequence_database_type:
+  -sequence_database_type
+  #if " " in str($param_sequence_database_type):
+    "$param_sequence_database_type"
+  #else
+    $param_sequence_database_type
+  #end if
+#end if
+#if $param_search_file:
+  -search_file $param_search_file
+#end if
+#if $param_params_file:
+  -params_file $param_params_file
+#end if
+#if $param_precursor_mz_tolerance:
+  -precursor_mz_tolerance $param_precursor_mz_tolerance
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_use_isotopically_averaged_mass:
+  -use_isotopically_averaged_mass
+#end if
+    #if $adv_opts.param_use_all_charge_states:
+  -use_all_charge_states
+#end if
+    #if $adv_opts.param_user_mod_file:
+  -user_mod_file $adv_opts.param_user_mod_file
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_spectra_files" type="data" format="mzml,mzxml,mzData,dta,msp" multiple="true" optional="False" size="30" label="File names(s) of spectra to be searched" help="(-spectra_files) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_library_file" type="data" format="splib" optional="False" label="Specify library file" help="(-library_file) "/>
+    <param name="param_sequence_database_file" type="data" format="fasta" optional="True" label="The sequence database" help="(-sequence_database_file) "/>
+    <param name="param_sequence_database_type" display="radio" type="select" optional="False" value="AA" label="Specify type of sequence database" help="(-sequence_database_type) ">
+      <option value="DNA">DNA</option>
+      <option value="AA" selected="true">AA</option>
+    </param>
+    <param name="param_search_file" type="data" format="txt,dat" optional="True" label="Only search a subset of the query spectra in the search file" help="(-search_file) "/>
+    <param name="param_params_file" type="data" format="params" optional="True" label="Read search options from file" help="(-params_file) All options set in the file will be overridden by command-line options, if specified"/>
+    <param name="param_precursor_mz_tolerance" type="float" min="0.0" optional="True" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="(-precursor_mz_tolerance) Monoisotopic mass is assumed"/>
+    <expand macro="advanced_options">
+      <param name="param_use_isotopically_averaged_mass" display="radio" type="boolean" truevalue="-use_isotopically_averaged_mass" falsevalue="" checked="false" optional="True" label="Use isotopically averaged mass instead of monoisotopic mass" help="(-use_isotopically_averaged_mass) "/>
+      <param name="param_use_all_charge_states" display="radio" type="boolean" truevalue="-use_all_charge_states" falsevalue="" checked="false" optional="True" label="Search library spectra of all charge states, i.e., ignore specified charge state (if any) of the query spectrum" help="(-use_all_charge_states) "/>
+      <param name="param_user_mod_file" type="data" format="txt" label="Specify name of user-defined modifications file" help="(-user_mod_file) Default is &quot;spectrast.usermods&quot;"/>
+      <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_output_files" format="txt"/>
+  </outputs>
+  <help>Interface to the SEARCH Mode of the SpectraST executable
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpectraSTSearchAdapter.html</help>
+</tool>
b
diff -r 000000000000 -r 369f340978e4 filetypes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/filetypes.txt Wed Aug 09 09:11:13 2017 -0400
b
@@ -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
b
diff -r 000000000000 -r 369f340978e4 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Aug 09 09:11:13 2017 -0400
b
@@ -0,0 +1,35 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="2.2">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>
b
diff -r 000000000000 -r 369f340978e4 readme.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.md Wed Aug 09 09:11:13 2017 -0400
[
@@ -0,0 +1,194 @@
+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/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. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it.
+
+    ```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 `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>
+    ```
+    
+
+ * 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.
+
b
diff -r 000000000000 -r 369f340978e4 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Wed Aug 09 09:11:13 2017 -0400
b
@@ -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>
b
diff -r 000000000000 -r 369f340978e4 test-data/DecoyDatabase_input.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DecoyDatabase_input.fasta Wed Aug 09 09:11:13 2017 -0400
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 369f340978e4 test-data/DecoyDatabase_output.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DecoyDatabase_output.fasta Wed Aug 09 09:11:13 2017 -0400
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 369f340978e4 tool.conf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool.conf Wed Aug 09 09:11:13 2017 -0400
b
@@ -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>