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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="InternalCalibration" name="InternalCalibration" version="1.12.0">
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3 <description>Applies an internal calibration.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">InternalCalibration</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>InternalCalibration
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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 -ref_peaks ${param_ref_peaks}
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15 -type ${param_type}
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16 -trafo ${param_trafo}
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17 -threads \${GALAXY_SLOTS:-24}
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18 -algorithm:mz_tolerance ${param_mz_tolerance}
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19 -algorithm:mz_tolerance_unit ${param_mz_tolerance_unit}
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20 -algorithm:rt_tolerance ${param_rt_tolerance}
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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" optional="False" label="input peak file " help="(-in)"/>
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24 <param name="param_ref_peaks" type="data" format="tabular,idXML" optional="True" label="input file containing reference m/z values (either as textfile with one m/z per line and no header or as idXML file)" help="(-ref_peaks)"/>
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25 <param name="param_type" type="select" optional="True" value="spectrumwise" label="The kind of internal calibration that should be applied." help="(-type)">
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26 <option value="spectrumwise">spectrumwise</option>
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27 <option value="global">global</option>
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28 </param>
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29 <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="1.0" label="Allowed tolerance between peak and reference m/z." help="(-mz_tolerance)"/>
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30 <param name="param_mz_tolerance_unit" type="select" optional="True" value="Da" label="Unit for mz_tolerance." help="(-mz_tolerance_unit)">
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31 <option value="Da">Da</option>
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32 <option value="ppm">ppm</option>
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33 </param>
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34 <param name="param_rt_tolerance" type="integer" value="10" label="Allowed tolerance between peak and reference rt." help="(-rt_tolerance)"/>
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35 </inputs>
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36 <outputs>
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37 <data name="param_out" label="output file " format="featureXML">
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38 <change_format>
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39 <when input="param_out_type" value="mzML" format="mzML"/>
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40 </change_format>
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41 </data>
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42 <data name="param_trafo" label="output transformation file (only for global calibration)" format="data"/>
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43 </outputs>
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44 <help>**What it does**
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45
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46 Applies an internal calibration.
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47
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48
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49 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html
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50
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51 @REFERENCES@
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52 </help>
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53 </tool>
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