comparison XFDR.xml @ 6:9a6e3bb0f358 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

5:e38e1a7af019

    <param name="uniquexl" argument="-uniquexl" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate statistics based only on unique IDs" help="For a set of IDs from equal candidates (same pair of peptides, modifications and cross-linked positions), only the highest scoring hit will be considered. By default the score distribution will be estimated using all 1st ranked candidates"/>
    <param name="no_qvalues" argument="-no_qvalues" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not transform simple FDR to q-values" help=""/>
    <param name="minscore" argument="-minscore" type="float" optional="true" value="-10.0" label="Minimum score to be considered for FDR calculation" help="A number lower than the lowest score will effectively disable this filter"/>
    <param name="binsize" argument="-binsize" type="float" optional="true" min="1e-15" value="0.0001" label="Bin size for the cumulative histograms for score distributions" help="Should be about the same size as the smallest expected difference between scores. Smaller numbers will make XFDR more robust, but much slower. Negative numbers are not allowed. Should only be changed if the range of the main score changes or another score than the OpenPepXL score is used"/>
    <expand macro="adv_opts_macro">
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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" multiple="true" label="Optional outputs" optional="false">
      <option value="out_idXML_FLAG">out_idXML (Enables the test mode (needed for internal use only))</option>
      <option value="out_mzIdentML_FLAG">out_mzIdentML (Enables the test mode (needed for internal use only))</option>
      <option value="out_xquest_FLAG">out_xquest (Enables the test mode (needed for internal use only))</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_idXML" label="${tool.name} on ${on_string}: out_idXML" format="idxml">

    <expand macro="manutest_XFDR"/>
  </tests>
  <help><![CDATA[Calculates false discovery rate estimates on crosslink identifications


For more information, visit http://www.openms.de/documentation/TOPP_XFDR.html]]></help>
  <expand macro="references"/>
</tool>

6:9a6e3bb0f358

    <param name="uniquexl" argument="-uniquexl" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate statistics based only on unique IDs" help="For a set of IDs from equal candidates (same pair of peptides, modifications and cross-linked positions), only the highest scoring hit will be considered. By default the score distribution will be estimated using all 1st ranked candidates"/>
    <param name="no_qvalues" argument="-no_qvalues" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not transform simple FDR to q-values" help=""/>
    <param name="minscore" argument="-minscore" type="float" optional="true" value="-10.0" label="Minimum score to be considered for FDR calculation" help="A number lower than the lowest score will effectively disable this filter"/>
    <param name="binsize" argument="-binsize" type="float" optional="true" min="1e-15" value="0.0001" label="Bin size for the cumulative histograms for score distributions" help="Should be about the same size as the smallest expected difference between scores. Smaller numbers will make XFDR more robust, but much slower. Negative numbers are not allowed. Should only be changed if the range of the main score changes or another score than the OpenPepXL score is used"/>
    <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="out_idXML_FLAG">out_idXML (Output as idXML file)</option>
      <option value="out_mzIdentML_FLAG">out_mzIdentML (Output as mzIdentML file)</option>
      <option value="out_xquest_FLAG">out_xquest (Output as xquest.xml file)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_idXML" label="${tool.name} on ${on_string}: out_idXML" format="idxml">

    <expand macro="manutest_XFDR"/>
  </tests>
  <help><![CDATA[Calculates false discovery rate estimates on crosslink identifications


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