<tool id="openms_peak_file_filter" version="0.1.0" name="mzML File Filter">
  <description>
    Extract portions of peak lists.
  </description>
  <requirements>
    <requirement type="package">openms</requirement>
  </requirements>
  <command interpreter="python">
    openms_wrapper.py --executable 'FileFilter' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
#if $mz.specify
mz=${mz.min}:${mz.max}
#end if
#if $rt.specify
rt=${rt.min}:${rt.max}
#end if
#if $intensity.specify
int=${intensity.min}:${intensity.max}
#end if
sn=${signal_to_noise}
in=${in}
in_type=mzML
out=${out}
out_type=mzML
</configfile>
  </configfiles>
  <inputs>
    <param format="mzml" name="in" type="data" label="Input mzML File"/>
    <param type="float" name="signal_to_noise" label="Minimum signal-to-noise ratio" value="0" />
    <conditional name="mz">
      <param type="boolean" name="specify" label="Filter by m/z" />
      <when value="true">
        <param type="float" name="min" label="Minimum m/z (optional)" optional="true" value="" />
        <param type="float" name="max" label="Maximum m/z (optional)" optional="true" value="" />
      </when>
    </conditional>
    <conditional name="rt">
      <param type="boolean" name="specify" label="Filter by retention time" />
      <when value="true">
        <param type="float" name="min" label="Minimum retention time (optional)" optional="true" value="" />
        <param type="float" name="max" label="Maximum retention (optional)" optional="true" value="" />
      </when>
    </conditional>
    <conditional name="intensity">
      <param type="boolean" name="specify" label="Filter by intensity" />
      <when value="true">
        <param type="float" name="min" label="Minimum intensity (optional)" optional="true" value="" />
        <param type="float" name="max" label="Maximum intensity (optional)" optional="true" value="" />
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="mzml" name="out" />
  </outputs>
  <help>
**What it does**

Extracts portions of the data from an mzML.

**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>