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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="InternalCalibration" name="InternalCalibration" version="2.0.0">
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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 #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_ref_peaks:
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19 -ref_peaks $param_ref_peaks
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20 #end if
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21 #if $param_type:
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22 -type
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23 #if " " in str($param_type):
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24 "$param_type"
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25 #else
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26 $param_type
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27 #end if
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28 #end if
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29 #if $param_trafo:
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30 -trafo $param_trafo
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31 #end if
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32 -threads \${GALAXY_SLOTS:-24}
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33 #if $param_algorithm_mz_tolerance:
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34 -algorithm:mz_tolerance $param_algorithm_mz_tolerance
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35 #end if
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36 #if $param_algorithm_mz_tolerance_unit:
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37 -algorithm:mz_tolerance_unit
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38 #if " " in str($param_algorithm_mz_tolerance_unit):
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39 "$param_algorithm_mz_tolerance_unit"
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40 #else
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41 $param_algorithm_mz_tolerance_unit
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42 #end if
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43 #end if
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44 #if $param_algorithm_rt_tolerance:
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45 -algorithm:rt_tolerance $param_algorithm_rt_tolerance
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46 #end if
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47 #if $adv_opts.adv_opts_selector=='advanced':
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48 #if $adv_opts.param_force:
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49 -force
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50 #end if
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51 #end if
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52 </command>
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53 <inputs>
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54 <param name="param_in" type="data" format="featurexml,mzml" optional="False" label="input peak file" help="(-in) "/>
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55 <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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56 <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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57 <option value="spectrumwise">spectrumwise</option>
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58 <option value="global">global</option>
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59 </param>
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60 <param name="param_algorithm_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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61 <param name="param_algorithm_mz_tolerance_unit" type="select" optional="True" value="Da" label="Unit for mz_tolerance" help="(-mz_tolerance_unit) ">
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62 <option value="Da">Da</option>
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63 <option value="ppm">ppm</option>
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64 </param>
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65 <param name="param_algorithm_rt_tolerance" type="integer" value="10" label="Allowed tolerance between peak and reference rt" help="(-rt_tolerance) "/>
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66 <expand macro="advanced_options">
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67 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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68 </expand>
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69 </inputs>
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70 <outputs>
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71 <data name="param_out" metadata_source="param_in" format="input"/>
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72 <data name="param_trafo" format="trafoxml"/>
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73 </outputs>
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74 <help>**What it does**
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75
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76 Applies an internal calibration.
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77
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78
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79 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html</help>
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80 <expand macro="references"/>
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81 </tool>
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