view export.xml @ 0:201a15633354 draft default tip

Initial commit.

<tool id="mzmatch_export" version="0.1.0" name="Peakml Export">
  <description>
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    mzmatch_wrapper.py --executable 'convert.ConvertToText' --config $config
  </command>
  <configfiles>
    <configfile name="config">-i $input1 -o $output</configfile>
  </configfiles>
  <inputs>
    <param name="input1" label="Input" type="data" format="peakml" />
  </inputs>
  <outputs>
    <data format="tabular" name="output" />
  </outputs>
  <help>
**What it does**

Converts the contents of a PeakML file to a tab-separated text file. In order to make the file useable in a spreadsheet environment, only the top-level data for each measurement is given in the file.

**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>