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1 <tool id="openms_feature_finder_raw" version="0.1.0" name="Feature Finder (Raw)">
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2 <description>
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3 Identifies peptide features in raw (i.e. profile) LC-MS data.
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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 'FeatureFinderRaw' --config $config
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12 </command>
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13 <configfiles>
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14 <configfile name="config">[simple_options]
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15 in=$input1
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16 out=$output
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17 sample!charge=${min_charge}:${max_charge}
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18 sample!peaks_per_peptide=${min_peaks_per_peptide}:${max_peaks_per_peptide}
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19 algorithm!rt_threshold=$rt_threshold
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20 algorithm!rt_min=$rt_min
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21 algorithm!intensity_cutoff=$intensity_cutoff
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22 algorithm!intensity_correlation=$intensity_correlation
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23 algorithm!model_deviation=$model_deviation
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24 </configfile>
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25 </configfiles>
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26 <inputs>
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27 <param name="input1" label="mzML Input" type="data" format="mzml" />
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28 <expand macro="raw_feature_finder_params" />
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29 </inputs>
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30 <outputs>
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31 <data format="featurexml" name="output" />
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32 </outputs>
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33 <help>
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34 **What it does**
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35
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36 FeatureFinderRaw is a tool for the identification of peptide features in profile LC-MS data.
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37
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38 **Citation**
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39
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40 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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41
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42 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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43 </help>
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44 </tool>
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