<tool id="mzmatch_extract_background_ions" version="0.1.0" name="Extract Background Ions">
  <description>
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    mzmatch_wrapper.py 
    --executable '__SHELL__' --config $setup
    --executable 'ExtractBackgroundIons' --config $config
  </command>
  <configfiles>
    <configfile name="setup">ln -s $input1 input.${input1.ext}</configfile>
    <configfile name="config">-ppm $ppm -i input.${input1.ext} -o $output -threshold $threshold</configfile>
  </configfiles>
  <inputs>
    <param name="input1" label="Input" type="data" format="mzml,mzxml" />
    <param name="ppm" label="ppm" value="3" type="float" help="The accuracy of the measurement in parts-per-milion. This value is used for the collection of the data-points belonging to a background ion and needs to be reasonable for the equipment used to make the measurement (the LTQ-Orbitrap manages approximatetly 3 ppm)." />
    <param name="threshold" type="float" value="0.02" label="Treshold" help="The percentage (a value between 0 and 1) of scans that minimally need to contain a measurement." />
  </inputs>
  <outputs>
    <data format="peakml" name="output" />
  </outputs>
  <help>
**What it does**

Extracts background ions (x-axis: RT; y-axis: Intensity) from 2D mass spectrometry data (LC/MS or GC/MS). The raw data is loaded from the open standard file formats (mzML, mzXML or mzData) and all of the individidual mass traces (M/Z +/- ppm over the whole scan range) are retrieved. A mass trace is retained when it is present in more than the given percentage of scans (option 'threshold').

The resulting output file is in PeakML-format, containing a list of all the extracted background ions.

**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>