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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="BaselineFilter" name="BaselineFilter" version="2.0.0">
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3 <description>Removes the baseline from profile spectra using a top-hat filter.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">BaselineFilter</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>BaselineFilter
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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 #if $param_struc_elem_length:
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19 -struc_elem_length $param_struc_elem_length
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20 #end if
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21 #if $param_struc_elem_unit:
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22 -struc_elem_unit
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23 #if " " in str($param_struc_elem_unit):
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24 "$param_struc_elem_unit"
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25 #else
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26 $param_struc_elem_unit
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27 #end if
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28 #end if
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29 #if $param_method:
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30 -method
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31 #if " " in str($param_method):
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32 "$param_method"
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33 #else
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34 $param_method
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35 #end if
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36 #end if
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37 -threads \${GALAXY_SLOTS:-24}
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38 #if $adv_opts.adv_opts_selector=='advanced':
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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_struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help="(-struc_elem_length) "/>
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47 <param name="param_struc_elem_unit" type="select" optional="True" value="Thomson" label="Unit of 'struc_elem_length' paramete" help="(-struc_elem_unit) ">
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48 <option value="Thomson">Thomson</option>
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49 <option value="DataPoints">DataPoints</option>
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50 </param>
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51 <param name="param_method" type="select" optional="True" value="tophat" label="The name of the morphological filter to be applied" help="(-method) If you are unsure, use the default">
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52 <option value="identity">identity</option>
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53 <option value="erosion">erosion</option>
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54 <option value="dilation">dilation</option>
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55 <option value="opening">opening</option>
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56 <option value="closing">closing</option>
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57 <option value="gradient">gradient</option>
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58 <option value="tophat">tophat</option>
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59 <option value="bothat">bothat</option>
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60 <option value="erosion_simple">erosion_simple</option>
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61 <option value="dilation_simple">dilation_simple</option>
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62 </param>
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63 <expand macro="advanced_options">
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64 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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65 </expand>
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66 </inputs>
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67 <outputs>
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68 <data name="param_out" format="mzml"/>
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69 </outputs>
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70 <help>**What it does**
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71
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72 Removes the baseline from profile spectra using a top-hat filter.
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73
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74
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75 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_BaselineFilter.html</help>
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76 <expand macro="references"/>
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77 </tool>
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