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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="BaselineFilter" name="BaselineFilter" version="1.12.0">
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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 -in ${param_in}
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13 -out ${param_out}
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14 -struc_elem_length ${param_struc_elem_length}
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15 -struc_elem_unit ${param_struc_elem_unit}
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16 -method ${param_method}
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17 -threads \${GALAXY_SLOTS:-24}
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18 </command>
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19 <inputs>
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20 <param name="param_in" type="data" format="mzML" optional="False" label="input raw data file " help="(-in)"/>
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21 <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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22 <param name="param_struc_elem_unit" type="select" optional="True" value="Thomson" label="Unit of 'struc_elem_length' parameter." help="(-struc_elem_unit)">
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23 <option value="Thomson">Thomson</option>
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24 <option value="DataPoints">DataPoints</option>
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25 </param>
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26 <param name="param_method" type="select" optional="True" value="tophat" label="The name of the morphological filter to be applied. If you are unsure, use the default." help="(-method)">
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27 <option value="identity">identity</option>
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28 <option value="erosion">erosion</option>
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29 <option value="dilation">dilation</option>
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30 <option value="opening">opening</option>
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31 <option value="closing">closing</option>
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32 <option value="gradient">gradient</option>
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33 <option value="tophat">tophat</option>
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34 <option value="bothat">bothat</option>
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35 <option value="erosion_simple">erosion_simple</option>
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36 <option value="dilation_simple">dilation_simple</option>
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37 </param>
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38 </inputs>
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39 <outputs>
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40 <data name="param_out" label="output raw data file " format="mzML"/>
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41 </outputs>
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42 <help>**What it does**
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43
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44 Removes the baseline from profile spectra using a top-hat filter.
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45
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46
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47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_BaselineFilter.html
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48
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49 @REFERENCES@
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50 </help>
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51 </tool>
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