annotate file_info.xml @ 2:cf0d72c7b482 draft

Update.

<tool id="openms_file_info" version="0.1.0" name="File Info">
  <description>
    Shows basic information about the file, such as data ranges and file type.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_wrapper.py --executable 'FileInfo' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
m=${m}
p=${p}
s=${s}
d=${d}
in=${in}
in_type=${in.ext}
out=${out}
</configfile>
  </configfiles>
  <inputs>
    <param format="mzxml,mzml,mgf,pepxml,idxml" name="in" type="data" label="Input Mass Spec Related File"/>
    <param type="boolean" name="m" label="Show meta information about the whole experiment" />
    <param type="boolean" name="p" label="Shows data processing information" />
    <param type="boolean" name="s" label="Computes a five-number statistics of intensities, qualities, and widths" />
    <param type="boolean" name="d" label="Show detailed listing of all spectra and chromatograms (peak files only)" />
    <param type="boolean" name="c" label="Check for corrupt data in the file (peak files only)" />
  </inputs>
  <outputs>
    <data format="txt" name="out" />
  </outputs>
  <help>
**What it does**

Shows basic information about the file, such as data ranges and file type.

**Citation**

For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``

If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
  </help>
</tool>