comparison SpectraSTSearchAdapter.xml @ 10:27ddea86fe90 draft

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

9:7e2e9379aec7

  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"executable": "spectrast", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="spectra_files" argument="-spectra_files" type="data" format="dta,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,msp,mzdata,mzml,mzxml data sets(s)"/>
    <param name="output_files_type" type="select" optional="false" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)">
      <option value="txt">txt</option>
      <option value="tsv">tabular (tsv)</option>
      <option value="pep.xml">pepxml (pep.xml)</option>
      <option value="xml">xml</option>
      <option value="pepXML">pepxml</option>
      <option value="html">html</option>
    </param>
    <param name="library_file" argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/>
    <param name="sequence_database_file" argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/>

    <param name="precursor_mz_tolerance" argument="-precursor_mz_tolerance" type="float" optional="true" min="0.0" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="Monoisotopic mass is assumed"/>
    <expand macro="adv_opts_macro">
      <param name="use_isotopically_averaged_mass" argument="-use_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/>
      <param name="use_all_charge_states" argument="-use_all_charge_states" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search library spectra of all charge states" help="i.e., ignore specified charge state (if any) of the query spectrum"/>
      <param name="user_mod_file" argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is &quot;spectrast.usermods&quot; select txt data sets(s)"/>
      <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>
    <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">

    <expand macro="manutest_SpectraSTSearchAdapter"/>
  </tests>
  <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable


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

10:27ddea86fe90

  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"executable": "spectrast", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="spectra_files" argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
    <param name="output_files_type" type="select" optional="false" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)">
      <option value="txt">txt</option>
      <option value="tsv">tabular (tsv)</option>
      <option value="pep.xml">pepxml (pep.xml)</option>
      <option value="pepXML">pepxml</option>
      <option value="html">html</option>
    </param>
    <param name="library_file" argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/>
    <param name="sequence_database_file" argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/>

    <param name="precursor_mz_tolerance" argument="-precursor_mz_tolerance" type="float" optional="true" min="0.0" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="Monoisotopic mass is assumed"/>
    <expand macro="adv_opts_macro">
      <param name="use_isotopically_averaged_mass" argument="-use_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/>
      <param name="use_all_charge_states" argument="-use_all_charge_states" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search library spectra of all charge states" help="i.e., ignore specified charge state (if any) of the query spectrum"/>
      <param name="user_mod_file" argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is &quot;spectrast.usermods&quot; select txt data sets(s)"/>
      <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>
    <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">

    <expand macro="manutest_SpectraSTSearchAdapter"/>
  </tests>
  <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable


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