<tool id="msconvert" name="msconvert" version="@VERSION@.4">
    <description>Convert and/or filter mass spectrometry files</description>
    <macros>
        <import>msconvert_macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">msconvert</xref>
    </xrefs>
    <requirements>
        <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container>
    </requirements>
    <stdio>
        <regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." />
    </stdio>
    <expand macro="msconvertCommand" />
    <inputs>
        <param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" />
        <expand macro="msconvertInputParameters" />
    </inputs>
    <expand macro="msconvertOutput" />
    <tests>
        <expand macro="msconvert_tests" />
    </tests>
    <help><![CDATA[
**What it does**

Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.

You can view the original documentation here_.

.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
]]></help>
    <expand macro="citations" />
</tool>