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1 <tool id="openms_peak_file_convert" version="0.1.0" name="Peak List File Converter">
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2 <description>
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3 Converts between different MS file formats.
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4 </description>
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5 <requirements>
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6 <requirement type="package">openms</requirement>
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7 </requirements>
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8 <command interpreter="python">
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9 openms_wrapper.py --executable 'FileConverter' --config $config
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10 </command>
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11 <configfiles>
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12 <configfile name="config">[simple_options]
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13 in=${in}
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14 in_type=${in.ext}
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15 out=${out}
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16 out_type=${out_format}
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17 </configfile>
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18 </configfiles>
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19 <inputs>
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20 <param format="mzml,mgf,mzxml,ms2" name="in" type="data" label="Input mzML File"/>
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21 <param type="select" name="out_format" label="Output Type">
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22 <option value="mzml">mzML</option>
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23 <option value="mzxml">mzXML</option>
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24 <option value="mgf">MGF</option>
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25 <option value="ms2">MS2</option>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data format="mzml" name="out">
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30 <change_format>
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31 <when input="out_format" value="mzxml" format="mzxml" />
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32 <when input="out_format" value="mgf" format="mgf" />
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33 <when input="out_format" value="ms2" format="ms2" />
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34 </change_format>
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35 </data>
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36 </outputs>
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37 <help>
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38 **What it does**
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39
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40 Extracts portions of the data from an mzML.
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41
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42 **Citation**
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43
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44 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.``
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45
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46 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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47 </help>
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48 </tool>
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