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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="NoiseFilterSGolay" name="NoiseFilterSGolay" version="2.0.0">
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3 <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">NoiseFilterSGolay</token>
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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="requirements"/>
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10 <command>NoiseFilterSGolay
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11
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12 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 -threads \${GALAXY_SLOTS:-24}
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19 #if $param_algorithm_frame_length:
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20 -algorithm:frame_length $param_algorithm_frame_length
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21 #end if
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22 #if $param_algorithm_polynomial_order:
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23 -algorithm:polynomial_order $param_algorithm_polynomial_order
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24 #end if
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25 #if $adv_opts.adv_opts_selector=='advanced':
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26 #if $adv_opts.param_processOption:
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27 -processOption
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28 #if " " in str($adv_opts.param_processOption):
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29 "$adv_opts.param_processOption"
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30 #else
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31 $adv_opts.param_processOption
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32 #end if
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33 #end if
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34 #if $adv_opts.param_force:
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35 -force
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36 #end if
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37 #end if
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38 </command>
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39 <inputs>
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40 <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/>
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41 <param name="param_algorithm_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="(-frame_length) <br>This number has to be uneven. If it is not, 1 will be added"/>
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42 <param name="param_algorithm_polynomial_order" type="integer" value="4" label="Order or the polynomial that is fitted" help="(-polynomial_order) "/>
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43 <expand macro="advanced_options">
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44 <param name="param_processOption" type="select" optional="True" value="inmemory" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="(-processOption) ">
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45 <option value="inmemory">inmemory</option>
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46 <option value="lowmemory">lowmemory</option>
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47 </param>
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48 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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49 </expand>
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50 </inputs>
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51 <outputs>
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52 <data name="param_out" format="mzml"/>
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53 </outputs>
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54 <help>**What it does**
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55
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56 Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.
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57
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58
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59 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterSGolay.html</help>
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60 <expand macro="references"/>
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61 </tool>
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