<tool id="mzmatch_noise_filter" version="0.1.0" name="Noise Filter">
  <description>
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    mzmatch_wrapper.py --executable 'filter.NoiseFilter' --config $config
  </command>
  <configfiles>
    <configfile name="config">-i $input1 -o $output -rejected $output_rejected #if $codadw.specify # -codadw $codadw.codadw #end if#</configfile>
  </configfiles>
  <inputs>
    <param name="input1" label="Input" type="data" format="peakml" />
    <conditional name="codadw">
      <param name="specify" label="Specify CoDA-DW Filter" type="boolean" />
      <when value="true">
        <param name="codadw" type="float" label="CoDA-DW Threshold" value="0.8" />
      </when>
      <when value="false">
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="peakml" name="output" label="Noise Filtered ${on_string}" />
    <data format="peakml" name="output_rejected" label="Noise Filtered Rejected ${on_string}" />
  </outputs>
  <help>
**What it does**

Filters noise from PeakML files, containing mass chromatograms at the lowest level. When the file contains a list of sets of mass chromatograms, the maximum score for the used method is calculated and compared to the given threshold. This is the best approach, as we expect that high quality can match up to low quality signals at the same mass and retention time. Only those entries scoring above the given threshold are stored in the output file. The rejected can be stored in a separate file (option 'rejected') for inspection or recovery.

The option 'codadw' can be used to set the threshold for the CoDA Durbin-Watson noise filtering approach. Normally the Durbin-Watson criterion results in a value between 0 and 4, where higher means a large amount of periodicity in the signal and lower vica versa. For mass chromatograms we expect little periodicity in the signal, thus a lower value is preferable. However, in order to preserve unity in our quality scores the CoDA-DW score is scaled between 0..1, where higher is better (less periodicity in the signal). As a general rule-of-thumb, for high quality mass chromatograms a score >0.8 is expected.

Remarks:
- CoDA-DW is scaled between 0..1, where higher is better mass chromatogram quality.

**Citation**

For the underlying tool, please cite ``PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis. Richard A. Scheltema, Andris Jankevics, Ritsert C. Jansen, Morris A. Swertz, and Rainer Breitling. Analytical Chemistry 2011 83 (7), pp 2786-2793``

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