comparison SimpleSearchEngine.xml @ 13:da78f97a6dda draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

12:4ef2f946290d

<?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="SimpleSearchEngine" name="SimpleSearchEngine" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Annotates MS/MS spectra using SimpleSearchEngine.</description>
  <macros>
    <token name="@EXECUTABLE@">SimpleSearchEngine</token>
    <import>macros.xml</import>
    <import>macros_autotest.xml</import>
    <import>macros_test.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@

  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
    <param name="database" argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
    <section name="Search" title="" help="" expanded="false">
      <param name="enzyme" argument="-Search:enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help="">
        <option value="Trypsin" selected="true">Trypsin</option>
        <option value="Lys-C/P">Lys-C/P</option>
        <option value="PepsinA">PepsinA</option>
        <option value="TrypChymo">TrypChymo</option>
        <option value="Trypsin/P">Trypsin/P</option>
        <option value="no cleavage">no cleavage</option>
        <option value="unspecific cleavage">unspecific cleavage</option>
        <option value="Arg-C/P">Arg-C/P</option>
        <option value="V8-DE">V8-DE</option>
        <option value="V8-E">V8-E</option>
        <option value="leukocyte elastase">leukocyte elastase</option>
        <option value="proline endopeptidase">proline endopeptidase</option>
        <option value="Arg-C">Arg-C</option>
        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
        <option value="CNBr">CNBr</option>
        <option value="Formic_acid">Formic_acid</option>
        <option value="Lys-C">Lys-C</option>
        <option value="Lys-N">Lys-N</option>
        <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
        <option value="Glu-C+P">Glu-C+P</option>
        <option value="PepsinA + P">PepsinA + P</option>
        <option value="cyanogen-bromide">cyanogen-bromide</option>
        <option value="Clostripain/P">Clostripain/P</option>
        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
        <option value="2-iodobenzoate">2-iodobenzoate</option>
        <option value="iodosobenzoate">iodosobenzoate</option>
        <option value="staphylococcal protease/D">staphylococcal protease/D</option>
        <option value="Asp-N">Asp-N</option>
        <option value="Asp-N/B">Asp-N/B</option>
        <option value="Asp-N_ambic">Asp-N_ambic</option>
        <option value="Chymotrypsin">Chymotrypsin</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="decoys" argument="-Search:decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Should decoys be generated?" help=""/>
      <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
        <param name="mass_tolerance" argument="-Search:precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/>
        <param name="mass_tolerance_unit" argument="-Search:precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
          <option value="ppm" selected="true">ppm</option>
          <option value="Da">Da</option>
          <expand macro="list_string_san"/>
        </param>
        <param name="min_charge" argument="-Search:precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/>
        <param name="max_charge" argument="-Search:precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/>
        <param name="isotopes" argument="-Search:precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
          <expand macro="list_integer_valsan"/>
        </param>
      </section>
      <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false">
        <param name="mass_tolerance" argument="-Search:fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance" help=""/>
        <param name="mass_tolerance_unit" argument="-Search:fragment:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of fragment m" help="">
          <option value="ppm" selected="true">ppm</option>
          <option value="Da">Da</option>
          <expand macro="list_string_san"/>
        </param>
      </section>
      <section name="modifications" title="Modifications Options" help="" expanded="false">
        <param name="fixed" argument="-Search:modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
          <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>

          <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
          <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
          <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
          <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
          <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
          <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
          <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>

          <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
          <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
          <option value="ZGB (K)">ZGB (K)</option>
          <option value="ZGB (N-term)">ZGB (N-term)</option>
          <option value="ZQG (K)">ZQG (K)</option>
          <expand macro="list_string_san"/>
        </param>
        <param name="variable" argument="-Search:modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
          <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
          <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
          <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>

          <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
          <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
          <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
          <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
          <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
          <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
          <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>

          <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
          <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
          <option value="ZGB (K)">ZGB (K)</option>
          <option value="ZGB (N-term)">ZGB (N-term)</option>
          <option value="ZQG (K)">ZQG (K)</option>
          <expand macro="list_string_san"/>
        </param>
        <param name="variable_max_per_peptide" argument="-Search:modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
      </section>
      <section name="annotate" title="Annotation Options" help="" expanded="false">
        <param name="PSM" argument="-Search:annotate:PSM" multiple="true" type="select" optional="true" label="Annotations added to each PSM" help="">
          <option value="">default (nothing chosen)</option>
          <option value="fragment_mz_error_median_ppm">fragment_mz_error_median_ppm</option>
          <option value="precursor_mz_error_ppm">precursor_mz_error_ppm</option>
          <expand macro="list_string_san"/>
        </param>
      </section>
      <section name="peptide" title="Peptide Options" help="" expanded="false">
        <param name="min_size" argument="-Search:peptide:min_size" type="integer" optional="true" value="7" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
        <param name="max_size" argument="-Search:peptide:max_size" type="integer" optional="true" value="40" label="Maximum size a peptide must have after digestion to be considered in the search (0 = disabled)" help=""/>
        <param name="missed_cleavages" argument="-Search:peptide:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/>
        <param name="motif" argument="-Search:peptide:motif" type="text" optional="true" value="" label="If set, only peptides that contain this motif (provided as RegEx) will be considered" help="">
          <expand macro="list_string_san"/>
        </param>
      </section>
      <section name="report" title="Reporting Options" help="" expanded="false">
        <param name="top_hits" argument="-Search:report:top_hits" type="integer" optional="true" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/>
      </section>
    </section>
    <expand macro="adv_opts_macro">
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>

    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <expand macro="autotest_SimpleSearchEngine"/>
    <expand macro="manutest_SimpleSearchEngine"/>
  </tests>
  <help><![CDATA[Annotates MS/MS spectra using SimpleSearchEngine.


For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SimpleSearchEngine.html]]></help>
  <expand macro="references"/>
</tool>

13:da78f97a6dda

<?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="SimpleSearchEngine" name="SimpleSearchEngine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Annotates MS/MS spectra using SimpleSearchEngine.</description>
  <macros>
    <token name="@EXECUTABLE@">SimpleSearchEngine</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@

  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
    <param argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
    <section name="Search" title="" help="" expanded="false">
      <param name="enzyme" argument="-Search:enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
        <option value="Trypsin" selected="true">Trypsin</option>
        <option value="staphylococcal protease/D">staphylococcal protease/D</option>
        <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
        <option value="Glu-C+P">Glu-C+P</option>
        <option value="PepsinA + P">PepsinA + P</option>
        <option value="cyanogen-bromide">cyanogen-bromide</option>
        <option value="Clostripain/P">Clostripain/P</option>
        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
        <option value="CNBr">CNBr</option>
        <option value="Formic_acid">Formic_acid</option>
        <option value="Lys-C">Lys-C</option>
        <option value="Arg-C/P">Arg-C/P</option>
        <option value="Asp-N">Asp-N</option>
        <option value="Asp-N/B">Asp-N/B</option>
        <option value="PepsinA">PepsinA</option>
        <option value="TrypChymo">TrypChymo</option>
        <option value="Trypsin/P">Trypsin/P</option>
        <option value="V8-DE">V8-DE</option>
        <option value="V8-E">V8-E</option>
        <option value="leukocyte elastase">leukocyte elastase</option>
        <option value="proline endopeptidase">proline endopeptidase</option>
        <option value="no cleavage">no cleavage</option>
        <option value="unspecific cleavage">unspecific cleavage</option>
        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
        <option value="2-iodobenzoate">2-iodobenzoate</option>
        <option value="iodosobenzoate">iodosobenzoate</option>
        <option value="Arg-C">Arg-C</option>
        <option value="Lys-N">Lys-N</option>
        <option value="Lys-C/P">Lys-C/P</option>
        <option value="Asp-N_ambic">Asp-N_ambic</option>
        <option value="Chymotrypsin">Chymotrypsin</option>
        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
        <expand macro="list_string_san" name="enzyme"/>
      </param>
      <param name="decoys" argument="-Search:decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Should decoys be generated?" help=""/>
      <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
        <param name="mass_tolerance" argument="-Search:precursor:mass_tolerance" type="float" optional="true" value="10.0" label="+/- tolerance for precursor mass" help=""/>
        <param name="mass_tolerance_unit" argument="-Search:precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
          <option value="ppm" selected="true">ppm</option>
          <option value="Da">Da</option>
          <expand macro="list_string_san" name="mass_tolerance_unit"/>
        </param>
        <param name="min_charge" argument="-Search:precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/>
        <param name="max_charge" argument="-Search:precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/>
        <param name="isotopes" argument="-Search:precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
          <expand macro="list_integer_valsan" name="isotopes"/>
        </param>
      </section>
      <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false">
        <param name="mass_tolerance" argument="-Search:fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance" help=""/>
        <param name="mass_tolerance_unit" argument="-Search:fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment m" help="">
          <option value="ppm" selected="true">ppm</option>
          <option value="Da">Da</option>
          <expand macro="list_string_san" name="mass_tolerance_unit"/>
        </param>
      </section>
      <section name="modifications" title="Modifications Options" help="" expanded="false">
        <param name="fixed" argument="-Search:modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
          <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>

          <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
          <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
          <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
          <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
          <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
          <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
          <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>

          <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
          <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
          <option value="ZGB (K)">ZGB (K)</option>
          <option value="ZGB (N-term)">ZGB (N-term)</option>
          <option value="ZQG (K)">ZQG (K)</option>
          <expand macro="list_string_san" name="fixed"/>
        </param>
        <param name="variable" argument="-Search:modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
          <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
          <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
          <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>

          <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
          <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
          <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
          <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
          <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
          <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
          <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
          <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>

          <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
          <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
          <option value="ZGB (K)">ZGB (K)</option>
          <option value="ZGB (N-term)">ZGB (N-term)</option>
          <option value="ZQG (K)">ZQG (K)</option>
          <expand macro="list_string_san" name="variable"/>
        </param>
        <param name="variable_max_per_peptide" argument="-Search:modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
      </section>
      <section name="annotate" title="Annotation Options" help="" expanded="false">
        <param name="PSM" argument="-Search:annotate:PSM" multiple="true" type="select" optional="true" label="Annotations added to each PSM" help="">
          <option value="ALL" selected="true">ALL</option>
          <option value="fragment_mz_error_median_ppm">fragment_mz_error_median_ppm</option>
          <option value="precursor_mz_error_ppm">precursor_mz_error_ppm</option>
          <option value="matched_prefix_ions_fraction">matched_prefix_ions_fraction</option>
          <option value="matched_suffix_ions_fraction">matched_suffix_ions_fraction</option>
          <expand macro="list_string_san" name="PSM"/>
        </param>
      </section>
      <section name="peptide" title="Peptide Options" help="" expanded="false">
        <param name="min_size" argument="-Search:peptide:min_size" type="integer" optional="true" value="7" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
        <param name="max_size" argument="-Search:peptide:max_size" type="integer" optional="true" value="40" label="Maximum size a peptide must have after digestion to be considered in the search (0 = disabled)" help=""/>
        <param name="missed_cleavages" argument="-Search:peptide:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/>
        <param name="motif" argument="-Search:peptide:motif" type="text" optional="true" value="" label="If set, only peptides that contain this motif (provided as RegEx) will be considered" help="">
          <expand macro="list_string_san" name="motif"/>
        </param>
      </section>
      <section name="report" title="Reporting Options" help="" expanded="false">
        <param name="top_hits" argument="-Search:report:top_hits" type="integer" optional="true" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/>
      </section>
    </section>
    <expand macro="adv_opts_macro">
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>

    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests><!-- UTILS_SimpleSearchEngine_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="SimpleSearchEngine_1.mzML"/>
      <param name="database" value="SimpleSearchEngine_1.fasta"/>
      <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
      <section name="Search">
        <param name="enzyme" value="Trypsin"/>
        <param name="decoys" value="false"/>
        <section name="precursor">
          <param name="mass_tolerance" value="5.0"/>
          <param name="mass_tolerance_unit" value="ppm"/>
          <param name="min_charge" value="2"/>
          <param name="max_charge" value="5"/>
          <param name="isotopes" value="0 1"/>
        </section>
        <section name="fragment">
          <param name="mass_tolerance" value="0.3"/>
          <param name="mass_tolerance_unit" value="Da"/>
        </section>
        <section name="modifications">
          <param name="fixed"/>
          <param name="variable" value="Oxidation (M)"/>
          <param name="variable_max_per_peptide" value="2"/>
        </section>
        <section name="annotate">
          <param name="PSM" value="ALL"/>
        </section>
        <section name="peptide">
          <param name="min_size" value="7"/>
          <param name="max_size" value="40"/>
          <param name="missed_cleavages" value="1"/>
          <param name="motif" value=""/>
        </section>
        <section name="report">
          <param name="top_hits" value="1"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <!-- UTILS_SimpleSearchEngine_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="SimpleSearchEngine_1.mzML"/>
      <param name="database" value="SimpleSearchEngine_1.fasta"/>
      <output name="out" file="SimpleSearchEngine_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
      <section name="Search">
        <param name="enzyme" value="Trypsin"/>
        <param name="decoys" value="false"/>
        <section name="precursor">
          <param name="mass_tolerance" value="10.0"/>
          <param name="mass_tolerance_unit" value="ppm"/>
          <param name="min_charge" value="2"/>
          <param name="max_charge" value="5"/>
          <param name="isotopes" value="0 1"/>
        </section>
        <section name="fragment">
          <param name="mass_tolerance" value="10.0"/>
          <param name="mass_tolerance_unit" value="ppm"/>
        </section>
        <section name="modifications">
          <param name="fixed" value="Carbamidomethyl (C)"/>
          <param name="variable" value="Oxidation (M)"/>
          <param name="variable_max_per_peptide" value="2"/>
        </section>
        <section name="annotate">
          <param name="PSM" value="ALL"/>
        </section>
        <section name="peptide">
          <param name="min_size" value="7"/>
          <param name="max_size" value="40"/>
          <param name="missed_cleavages" value="1"/>
          <param name="motif" value=""/>
        </section>
        <section name="report">
          <param name="top_hits" value="1"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Annotates MS/MS spectra using SimpleSearchEngine.


For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SimpleSearchEngine.html]]></help>
  <expand macro="references"/>
</tool>