comparison OpenSwathDecoyGenerator.xml @ 11:3769d3a7e9ba draft

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

10:965413f29bf5

      <option value="TraML">traml</option>
      <option value="pqp">pqp</option>
      <option value="tsv">tabular (tsv)</option>
      <expand macro="list_string_san"/>
    </param>
    <param name="method" argument="-method" display="radio" type="select" optional="false" label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" help="">
      <option value="shuffle" selected="true">shuffle</option>
      <option value="pseudo-reverse">pseudo-reverse</option>
      <option value="reverse">reverse</option>
      <option value="shift">shift</option>
      <expand macro="list_string_san"/>

        <expand macro="list_string_san"/>
      </param>
      <param name="enable_detection_specific_losses" argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
      <param name="enable_detection_unspecific_losses" argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
      <param name="separate" argument="-separate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if decoys should not be appended to targets" help=""/>
      <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="true">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out">

    <expand macro="manutest_OpenSwathDecoyGenerator"/>
  </tests>
  <help><![CDATA[Generates decoys according to different models for a specific TraML


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

11:3769d3a7e9ba

      <option value="TraML">traml</option>
      <option value="pqp">pqp</option>
      <option value="tsv">tabular (tsv)</option>
      <expand macro="list_string_san"/>
    </param>
    <param name="method" argument="-method" display="radio" type="select" optional="false" label="Decoy generation method" help="">
      <option value="shuffle" selected="true">shuffle</option>
      <option value="pseudo-reverse">pseudo-reverse</option>
      <option value="reverse">reverse</option>
      <option value="shift">shift</option>
      <expand macro="list_string_san"/>

        <expand macro="list_string_san"/>
      </param>
      <param name="enable_detection_specific_losses" argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
      <param name="enable_detection_unspecific_losses" argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
      <param name="separate" argument="-separate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if decoys should not be appended to targets" help=""/>
      <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>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out">

    <expand macro="manutest_OpenSwathDecoyGenerator"/>
  </tests>
  <help><![CDATA[Generates decoys according to different models for a specific TraML


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