comparison OpenSwathDIAPreScoring.xml @ 7:9bf5470fb0bc draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

6:76e8df062c6d

    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathDIAPreScoring

#if $param_tr:
  -tr $param_tr
#end if
#if $param_out:

#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
    <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be applied">
      <sanitizer>
        <valid initial="string.printable">

    <data name="param_out" format="tabular"/>
  </outputs>
  <help>Scoring spectra using the DIA scores.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathDIAPreScoring.html</help>
</tool>

7:9bf5470fb0bc

    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[OpenSwathDIAPreScoring

#if $param_tr:
  -tr $param_tr
#end if
#if $param_out:

#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
]]></command>
  <inputs>
    <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
    <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be applied">
      <sanitizer>
        <valid initial="string.printable">

    <data name="param_out" format="tabular"/>
  </outputs>
  <help>Scoring spectra using the DIA scores.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_OpenSwathDIAPreScoring.html</help>
</tool>