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1 <tool id="openms_idxml_to_tabular" version="0.1.0" name="Export idXML to Tabular">
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2 <description>
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3 Converts identification engine file formats.
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio" />
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9 <expand macro="requires" />
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10 <command interpreter="python">
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11 openms_wrapper.py --executable 'TextExporter' --config $config
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12 </command>
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13 <configfiles>
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14 <configfile name="config">[simple_options]
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15 in=${in}
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16 out=${out}
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17 $dump_type
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18 id!first_dim_rt=$extra_rt
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19 </configfile>
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20 </configfiles>
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21 <inputs>
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22 <param format="idxml" name="in" type="data" label="Input Identification File"/>
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23 <param name="dump_type" type="select" label="Export type">
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24 <option value="">Run, peptide, and protein information</option>
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25 <option value="id!proteins_only=true">Run and protein information only</option>
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26 <option value="id!peptides_only=true">Peptide information only</option>
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27 </param>
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28 <param name="extra_rt" type="boolean" label="Include RT information (if present)" />
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29 </inputs>
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30 <outputs>
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31 <data format="tabular" name="out">
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32 </data>
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33 </outputs>
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34 <help>
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35 **What it does**
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36
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37 Converts idXML files to tabular.
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38
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39 **Citation**
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40
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41 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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42
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43 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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44 </help>
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45 </tool>
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