comparison MSGFPlusAdapter.xml @ 7:f0761deada39 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb

6:2244cc0ac5cd

#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
 ]]>
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml,mzxml,mgf,ms2" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/>
    <param name="param_database" type="data" format="fasta" optional="False" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="(-database) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
    <param name="param_add_decoys" display="radio" type="boolean" truevalue="-add_decoys" falsevalue="" checked="false" optional="True" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="(-add_decoys) This allows the calculation of FDRs, but should only be used if the database does not already contain decoys"/>
    <param name="param_precursor_mass_tolerance" type="float" value="10.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_mass_tolerance) "/>
    <param name="param_precursor_error_units" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_error_units) ">
      <option value="Da">Da</option>
      <option value="ppm" selected="true">ppm</option>
    </param>

      <param name="param_legacy_conversion" display="radio" type="boolean" truevalue="-legacy_conversion" falsevalue="" checked="false" optional="True" label="Use the indirect conversion of MS-GF+ results to idXML via export to TSV" help="(-legacy_conversion) Try this only if the default conversion takes too long or uses too much memory"/>
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="idxml"/>
    <data name="param_mzid_out" format="mzid"/>
  </outputs>
  <help>MS/MS database search using MS-GF+.


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

7:f0761deada39

#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
-threads "\${GALAXY_SLOTS:-1}"
 ]]>
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml,mzxml,mgf,ms2" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/>
    <param name="param_database" type="data" format="fasta" optional="False" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="(-database) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
    <param name="param_add_decoys" display="radio" type="boolean" truevalue="-add_decoys" falsevalue="" checked="false" optional="True" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="(-add_decoys) This allows the calculation of FDRs, but should only be used if the database does not already contain decoys. Decoys are marked by the prefix XXX_"/>
    <param name="param_precursor_mass_tolerance" type="float" value="10.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_mass_tolerance) "/>
    <param name="param_precursor_error_units" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_error_units) ">
      <option value="Da">Da</option>
      <option value="ppm" selected="true">ppm</option>
    </param>

      <param name="param_legacy_conversion" display="radio" type="boolean" truevalue="-legacy_conversion" falsevalue="" checked="false" optional="True" label="Use the indirect conversion of MS-GF+ results to idXML via export to TSV" help="(-legacy_conversion) Try this only if the default conversion takes too long or uses too much memory"/>
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="idxml" label="${tool.name} on ${on_string}: idxml"/>
    <data name="param_mzid_out" format="mzid" label=" ${tool.name} on ${on_string}: mzid"/>
  </outputs>
  <help>MS/MS database search using MS-GF+.


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