Mercurial > repos > galaxyp > openms_noisefiltergaussian

annotate NoiseFilterGaussian.xml @ 1:8357cd696719 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:07:14 -0400
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b6baace535ae 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="NoiseFilterGaussian" name="NoiseFilterGaussian" version="2.2.0">
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5 <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">NoiseFilterGaussian</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>NoiseFilterGaussian
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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_gaussian_width:
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22 -algorithm:gaussian_width $param_algorithm_gaussian_width
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23 #end if
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24 #if $param_algorithm_ppm_tolerance:
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25 -algorithm:ppm_tolerance $param_algorithm_ppm_tolerance
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26 #end if
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27 #if $param_algorithm_use_ppm_tolerance:
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28 -algorithm:use_ppm_tolerance
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29 #end if
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30 #if $adv_opts.adv_opts_selector=='advanced':
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31 #if $adv_opts.param_processOption:
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32 -processOption
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33 #if " " in str($adv_opts.param_processOption):
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34 "$adv_opts.param_processOption"
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35 #else
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36 $adv_opts.param_processOption
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37 #end if
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38 #end if
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39 #if $adv_opts.param_force:
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40 -force
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41 #end if
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42 #end if
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43 </command>
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44 <inputs>
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45 <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/>
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46 <param name="param_algorithm_gaussian_width" type="float" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help="(-gaussian_width) "/>
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47 <param name="param_algorithm_ppm_tolerance" type="float" value="10.0" label="Gaussian width, depending on the m/z position" help="(-ppm_tolerance) &lt;br&gt;The higher the value, the wider the peak and therefore the wider the gaussian"/>
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48 <param name="param_algorithm_use_ppm_tolerance" display="radio" type="boolean" truevalue="-algorithm:use_ppm_tolerance" falsevalue="" checked="false" optional="True" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" help="(-use_ppm_tolerance) The gaussian is calculated in each step anew, so this is much slower"/>
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49 <expand macro="advanced_options">
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50 <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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51 <option value="inmemory" selected="true">inmemory</option>
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52 <option value="lowmemory">lowmemory</option>
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53 </param>
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54 <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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55 </expand>
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56 </inputs>
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57 <outputs>
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58 <data name="param_out" format="mzml"/>
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59 </outputs>
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60 <help>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
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61
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62
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63 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterGaussian.html</help>
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64 </tool>