comparison FileInfo.xml @ 13:e8dce5e07fa5 draft

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

12:32264aaa27b8

  <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="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,trafoxml" optional="false" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,trafoxml data sets(s)"/>
    <param name="m" argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
    <param name="p" argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
    <param name="s" argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/>
    <param name="d" argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/>
    <param name="c" argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/>
    <param name="v" argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/>
    <param name="i" argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/>
    <expand macro="adv_opts_macro">
      <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="out_tsv_FLAG">out_tsv (Enables the test mode (needed for internal use only))</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="txt"/>

    <expand macro="manutest_FileInfo"/>
  </tests>
  <help><![CDATA[Shows basic information about the file, such as data ranges and file type.


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

13:e8dce5e07fa5

  <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="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,trafoxml" optional="false" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,trafoxml data sets(s)"/>
    <param name="m" argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
    <param name="p" argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
    <param name="s" argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/>
    <param name="d" argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/>
    <param name="c" argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/>
    <param name="v" argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/>
    <param name="i" argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/>
    <expand macro="adv_opts_macro">
      <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_tsv_FLAG">out_tsv (Second optional output file)</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="txt"/>

    <expand macro="manutest_FileInfo"/>
  </tests>
  <help><![CDATA[Shows basic information about the file, such as data ranges and file type.


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