comparison PrecursorIonSelector.xml @ 11:fa7a58de2977 draft

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

10:fe761c27a561

#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <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="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/>
    <param name="ids" argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/>
    <param name="num_precursors" argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/>

      <param name="solver" argument="-solver" display="radio" type="select" optional="false" label="LP solver type" help="">
        <option value="GLPK" selected="true">GLPK</option>
        <option value="COINOR">COINOR</option>
        <expand macro="list_string_san"/>
      </param>
      <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_FLAG">out (std of the gauss curve)</option>
      <option value="next_feat_FLAG">next_feat (std of the gauss curve)</option>
      <option value="sim_results_FLAG">sim_results (std of the gauss curve)</option>
      <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="featurexml">

    <expand macro="manutest_PrecursorIonSelector"/>
  </tests>
  <help><![CDATA[PrecursorIonSelector


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

11:fa7a58de2977

#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "algorithm": {"Preprocessing": {"tmp_dir": "\$TMP_DIR"}}}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/>
    <param name="ids" argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/>
    <param name="num_precursors" argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/>

      <param name="solver" argument="-solver" display="radio" type="select" optional="false" label="LP solver type" help="">
        <option value="GLPK" selected="true">GLPK</option>
        <option value="COINOR">COINOR</option>
        <expand macro="list_string_san"/>
      </param>
      <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_FLAG">out (modified feature map)</option>
      <option value="next_feat_FLAG">next_feat (feature map (featureXML) file with the selected precursors)</option>
      <option value="sim_results_FLAG">sim_results (File containing the results of the simulation run)</option>
      <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="featurexml">

    <expand macro="manutest_PrecursorIonSelector"/>
  </tests>
  <help><![CDATA[PrecursorIonSelector


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