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1 <tool id="openms_noise_filter" version="0.1.0" name="Noise Filter">
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2 <description>
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3 Utilize a filter to reduce the noise in an MS experiment.
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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 #if $filter.type == "gaussian"
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10 #set $filter_exec = "NoiseFilterGaussian"
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11 #elif $filter.type == "sgolay"
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12 #set $filter_exec = "NoiseFilterSGolay"
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13 #end if
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14 openms_wrapper.py --executable '$filter_exec' --config $config
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15 </command>
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16 <configfiles>
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17 <configfile name="config">[simple_options]
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18 in=${in}
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19 out=${out}
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20 </configfile>
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21 </configfiles>
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22 <inputs>
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23 <param format="mzml" name="in" type="data" label="Input mzML"/>
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24 <conditional name="filter">
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25 <param type="select" name="type" label="Filter Type">
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26 <option value="gaussian">Gaussian</option>
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27 <option value="sgolay">Savitzky Golay</option>
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28 </param>
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29 </conditional>
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30 </inputs>
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31 <outputs>
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32 <data format="mzml" name="out" />
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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 TODO: Document
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38
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39 http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_NoiseFilterSGolay.html
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40 http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_NoiseFilterGaussian.html
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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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