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annotate NoiseFilterGaussian.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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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="2.0.0">
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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 -threads \${GALAXY_SLOTS:-24}
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22 #if $param_algorithm_gaussian_width:
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23 -algorithm:gaussian_width $param_algorithm_gaussian_width
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24 #end if
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25 #if $param_algorithm_ppm_tolerance:
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26 -algorithm:ppm_tolerance $param_algorithm_ppm_tolerance
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27 #end if
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28 #if $param_algorithm_use_ppm_tolerance:
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29 -algorithm:use_ppm_tolerance
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30 #end if
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31 #if $adv_opts.adv_opts_selector=='advanced':
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32 #if $adv_opts.param_processOption:
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33 -processOption
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34 #if &quot; &quot; in str($adv_opts.param_processOption):
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35 &quot;$adv_opts.param_processOption&quot;
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36 #else
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37 $adv_opts.param_processOption
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38 #end if
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39 #end if
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40 #if $adv_opts.param_force:
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41 -force
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42 #end if
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43 #end if
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44 </command>
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45 <inputs>
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46 <param format="mzml" help="(-in) " label="input raw data file" name="param_in" optional="False" type="data"/>
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47 <param help="(-gaussian_width) " label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" name="param_algorithm_gaussian_width" type="float" value="0.2"/>
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48 <param help="(-ppm_tolerance) &lt;br&gt;The higher the value, the wider the peak and therefore the wider the gaussian" label="Gaussian width, depending on the m/z position" name="param_algorithm_ppm_tolerance" type="float" value="10.0"/>
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49 <param checked="false" falsevalue="" help="(-use_ppm_tolerance) The gaussian is calculated in each step anew, so this is much slower" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" name="param_algorithm_use_ppm_tolerance" optional="True" truevalue="-algorithm:use_ppm_tolerance" type="boolean"/>
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50 <expand macro="advanced_options">
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51 <param help="(-processOption) " 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" name="param_processOption" optional="True" type="select" value="inmemory">
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52 <option value="inmemory">inmemory</option>
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53 <option value="lowmemory">lowmemory</option>
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54 </param>
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55 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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56 </expand>
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57 </inputs>
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58 <outputs>
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59 <data format="mzml" name="param_out"/>
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60 </outputs>
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61 <help>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
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63
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64 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterGaussian.html</help>
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65 </tool>