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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="MapRTTransformer" name="MapRTTransformer" version="1.12.0">
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3 <description>Applies retention time transformations to maps.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">MapRTTransformer</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>MapRTTransformer
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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 -trafo_in ${param_trafo_in}
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15 -trafo_out ${param_trafo_out}
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16 ${param_invert}
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17 -threads \${GALAXY_SLOTS:-24}
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18 -model:type ${param_type}
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19 ${param_symmetric_regression}
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20 -model:interpolated:interpolation_type ${param_interpolation_type}
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21 </command>
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22 <inputs>
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23 <param name="param_in" type="data" format="mzML,featureXML,consensusXML,idXML" optional="True" size="20" label="Input files to transform (separated by blanks)" help="(-in)"/>
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24 <param name="param_trafo_in" type="data" format="" optional="False" size="20" label="Transformations to apply (files separated by blanks)" help="(-trafo_in)"/>
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25 <param name="param_invert" type="boolean" truevalue="-invert true" falsevalue="-invert false" checked="false" optional="True" label="Invert transformations (approximatively) before applying them" help="(-invert)"/>
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26 <param name="param_type" type="select" optional="True" value="none" label="Type of model" help="(-type)">
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27 <option value="none">none</option>
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28 <option value="linear">linear</option>
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29 <option value="b_spline">b_spline</option>
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30 <option value="interpolated">interpolated</option>
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31 </param>
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32 <param name="param_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression true" falsevalue="-model:linear:symmetric_regression false" checked="false" optional="True" label="Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/>
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33 <param name="param_interpolation_type" type="select" optional="True" value="cspline" label="Type of interpolation to apply." help="(-interpolation_type)">
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34 <option value="linear">linear</option>
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35 <option value="cspline">cspline</option>
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36 <option value="akima">akima</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 files separated by blanks. Either this option or 'trafo_out' have to be provided. They can be used together." format="idXML">
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41 <change_format>
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42 <when input="param_out_type" value="mzML" format="mzML"/>
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43 <when input="param_out_type" value="featureXML" format="featureXML"/>
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44 <when input="param_out_type" value="consensusXML" format="consensusXML"/>
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45 </change_format>
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46 </data>
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47 <data name="param_trafo_out" label="Transformation output files separated by blanks. Either this option or 'out' have to be provided. They can be used together." format="data"/>
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48 </outputs>
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49 <help>**What it does**
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50
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51 Applies retention time transformations to maps.
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52
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53
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54 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html
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55
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56 @REFERENCES@
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57 </help>
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58 </tool>
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