Mercurial > repos > galaxyp > openms_noisefiltersgolay

annotate NoiseFilterSGolay.xml @ 0:ae2d145ecafc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 09:58:49 -0500
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ae2d145ecafc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
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4 <tool id="NoiseFilterSGolay" name="NoiseFilterSGolay" version="2.1.0">
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5 <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">NoiseFilterSGolay</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>NoiseFilterSGolay
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_algorithm_frame_length:
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22 -algorithm:frame_length $param_algorithm_frame_length
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23 #end if
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24 #if $param_algorithm_polynomial_order:
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25 -algorithm:polynomial_order $param_algorithm_polynomial_order
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26 #end if
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27 #if $adv_opts.adv_opts_selector=='advanced':
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28 #if $adv_opts.param_processOption:
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29 -processOption $adv_opts.param_processOption
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30 #end if
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31 #if $adv_opts.param_force:
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32 -force
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33 #end if
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34 #end if
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35 </command>
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36 <inputs>
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37 <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/>
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38 <param name="param_algorithm_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="(-frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added"/>
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39 <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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40 <expand macro="advanced_options">
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41 <param name="param_processOption" display="radio" type="select" optional="False" 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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42 <option value="inmemory" selected="true">inmemory</option>
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43 <option value="lowmemory">lowmemory</option>
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44 </param>
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45 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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46 </expand>
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47 </inputs>
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48 <outputs>
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49 <data name="param_out" format="mzml"/>
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50 </outputs>
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51 <help>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.
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52
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53
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54 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterSGolay.html</help>
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55 </tool>