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annotate BaselineFilter.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="BaselineFilter" name="BaselineFilter" version="2.0.0">
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5 <description>Removes the baseline from profile spectra using a top-hat filter.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">BaselineFilter</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>BaselineFilter
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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_struc_elem_length:
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22 -struc_elem_length $param_struc_elem_length
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23 #end if
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24 #if $param_struc_elem_unit:
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25 -struc_elem_unit
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26 #if &quot; &quot; in str($param_struc_elem_unit):
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27 &quot;$param_struc_elem_unit&quot;
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28 #else
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29 $param_struc_elem_unit
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30 #end if
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31 #end if
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32 #if $param_method:
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33 -method
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34 #if &quot; &quot; in str($param_method):
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35 &quot;$param_method&quot;
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36 #else
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37 $param_method
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38 #end if
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39 #end if
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40 -threads \${GALAXY_SLOTS:-24}
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41 #if $adv_opts.adv_opts_selector=='advanced':
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42 #if $adv_opts.param_force:
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43 -force
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44 #end if
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45 #end if
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46 </command>
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47 <inputs>
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48 <param format="mzml" help="(-in) " label="input raw data file" name="param_in" optional="False" type="data"/>
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49 <param help="(-struc_elem_length) " label="Length of the structuring element (should be wider than maximal peak width - see documentation)" name="param_struc_elem_length" type="float" value="3.0"/>
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50 <param help="(-struc_elem_unit) " label="Unit of 'struc_elem_length' paramete" name="param_struc_elem_unit" optional="True" type="select" value="Thomson">
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51 <option value="Thomson">Thomson</option>
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52 <option value="DataPoints">DataPoints</option>
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53 </param>
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54 <param help="(-method) If you are unsure, use the default" label="The name of the morphological filter to be applied" name="param_method" optional="True" type="select" value="tophat">
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55 <option value="identity">identity</option>
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56 <option value="erosion">erosion</option>
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57 <option value="dilation">dilation</option>
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58 <option value="opening">opening</option>
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59 <option value="closing">closing</option>
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60 <option value="gradient">gradient</option>
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61 <option value="tophat">tophat</option>
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62 <option value="bothat">bothat</option>
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63 <option value="erosion_simple">erosion_simple</option>
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64 <option value="dilation_simple">dilation_simple</option>
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65 </param>
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66 <expand macro="advanced_options">
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67 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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68 </expand>
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69 </inputs>
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70 <outputs>
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71 <data format="mzml" name="param_out"/>
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72 </outputs>
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73 <help>Removes the baseline from profile spectra using a top-hat filter.
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75
4
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76 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_BaselineFilter.html</help>
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77 </tool>