comparison SimpleSearchEngine.xml @ 7:3cec90deb64b draft

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

6:a3b09a079597

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

#if $param_in:
  -in $param_in
#end if
#if $param_database:

#end if
    #if $adv_opts.param_report_top_hits:
  -report:top_hits $adv_opts.param_report_top_hits
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
    <param name="param_database" type="data" format="fasta" optional="False" label="input file" help="(-database) "/>
    <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
      <option value="leukocyte elastase">leukocyte elastase</option>

  </inputs>
  <outputs>
    <data name="param_out" format="idxml"/>
  </outputs>
  <help>Annotates MS/MS spectra using SimpleSearchEngine.


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

7:3cec90deb64b

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

#if $param_in:
  -in $param_in
#end if
#if $param_database:

#end if
    #if $adv_opts.param_report_top_hits:
  -report:top_hits $adv_opts.param_report_top_hits
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
    <param name="param_database" type="data" format="fasta" optional="False" label="input file" help="(-database) "/>
    <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
      <option value="leukocyte elastase">leukocyte elastase</option>

  </inputs>
  <outputs>
    <data name="param_out" format="idxml"/>
  </outputs>
  <help>Annotates MS/MS spectra using SimpleSearchEngine.
  </help>
</tool>