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1 <tool id="openms_pepxml_protxml_merger" version="0.1.0" name="Merge idXML from PepXML and ProtXML">
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2 <description>
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3 </description>
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4 <requirements>
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5 <requirement type="package">openms</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8 openms_wrapper.py --executable 'IDMerger' --config $config
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9 </command>
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10 <configfiles>
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11 <configfile name="config">[simple_options]
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12 in="${pepxml} ${protxml}"
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13 out=${out}
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14 annotate_file_origin=${annotate_file_origin}
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15 pepxml_protxml=true
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16 </configfile>
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17 </configfiles>
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18 <inputs>
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19 <param format="idxml" name="pepxml" type="data" label="idXML from PepXML"/>
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20 <param format="idxml" name="protxml" type="data" label="idXML from ProtXML"/>
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21 <param type="boolean" name="annotate_file_origin" label="Annotate file origin" help="Store the original filename in each protein/peptide identification (MetaValue: file_origin)." />
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22 </inputs>
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23 <outputs>
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24 <data format="idxml" name="out" />
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25 </outputs>
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26 <help>
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27 **What it does**
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28
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29 Merge idXML files derived from a pepXML and corresponding protXML file.
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30
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31 **Citation**
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32
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33 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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34
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35 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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36 </help>
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37 </tool>
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