comparison IDScoreSwitcher.xml @ 15:eb0bc9c697ee draft

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

14:cecb51784c3a

    <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="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
    <param name="new_score" argument="-new_score" type="text" optional="false" value="" label="Name of the meta value to use as the new score" help="">
      <expand macro="list_string_san"/>
    </param>
    <param name="new_score_orientation" argument="-new_score_orientation" display="radio" type="select" optional="false" label="Orientation of the new score (are higher or lower values better?)" help="">
      <option value="lower_better">lower_better</option>
      <option value="higher_better">higher_better</option>
      <expand macro="list_string_san"/>
    </param>
    <param name="new_score_type" argument="-new_score_type" type="text" optional="true" value="" label="Name to use as the type of the new score (default: same as 'new_score')" help="">
      <expand macro="list_string_san"/>
    </param>
    <param name="old_score" argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help="">
      <expand macro="list_string_san"/>
    </param>
    <param name="proteins" argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/>
    <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="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" format="idxml"/>

    <expand macro="manutest_IDScoreSwitcher"/>
  </tests>
  <help><![CDATA[Switches between different scores of peptide or protein hits in identification data


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

15:eb0bc9c697ee

    <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="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
    <param name="proteins" argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/>
    <param name="new_score" argument="-new_score" type="text" optional="true" value="" label="Name of the meta value to use as the new score" help="">
      <expand macro="list_string_san"/>
    </param>
    <param name="new_score_orientation" argument="-new_score_orientation" display="radio" type="select" optional="true" label="Orientation of the new score (are higher or lower values better?)" help="">
      <option value="">default (nothing chosen)</option>
      <option value="lower_better">lower_better</option>
      <option value="higher_better">higher_better</option>
      <expand macro="list_string_san"/>
    </param>
    <param name="new_score_type" argument="-new_score_type" type="text" optional="true" value="" label="Name to use as the type of the new score (default: same as 'new_score')" help="">
      <expand macro="list_string_san"/>
    </param>
    <param name="old_score" argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help="">
      <expand macro="list_string_san"/>
    </param>
    <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>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>

    <expand macro="manutest_IDScoreSwitcher"/>
  </tests>
  <help><![CDATA[Switches between different scores of peptide or protein hits in identification data


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