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annotate InternalCalibration.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
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4 <tool id="InternalCalibration" name="InternalCalibration" version="2.0.0">
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5 <description>Applies an internal calibration.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">InternalCalibration</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>InternalCalibration
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_ref_peaks:
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22 -ref_peaks $param_ref_peaks
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23 #end if
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24 #if $param_type:
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25 -type
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26 #if &quot; &quot; in str($param_type):
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27 &quot;$param_type&quot;
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28 #else
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29 $param_type
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30 #end if
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31 #end if
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32 #if $param_trafo:
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33 -trafo $param_trafo
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34 #end if
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35 -threads \${GALAXY_SLOTS:-24}
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36 #if $param_algorithm_mz_tolerance:
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37 -algorithm:mz_tolerance $param_algorithm_mz_tolerance
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38 #end if
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39 #if $param_algorithm_mz_tolerance_unit:
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40 -algorithm:mz_tolerance_unit
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41 #if &quot; &quot; in str($param_algorithm_mz_tolerance_unit):
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42 &quot;$param_algorithm_mz_tolerance_unit&quot;
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43 #else
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44 $param_algorithm_mz_tolerance_unit
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45 #end if
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46 #end if
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47 #if $param_algorithm_rt_tolerance:
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48 -algorithm:rt_tolerance $param_algorithm_rt_tolerance
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49 #end if
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50 #if $adv_opts.adv_opts_selector=='advanced':
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51 #if $adv_opts.param_force:
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52 -force
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53 #end if
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54 #end if
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55 </command>
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56 <inputs>
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57 <param format="xml,mzml" help="(-in) " label="input peak file" name="param_in" optional="False" type="data"/>
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58 <param format="tabular,xml" help="(-ref_peaks) " label="input file containing reference m/z values (either as textfile with one m/z per line and no header or as idXML file)" name="param_ref_peaks" optional="True" type="data"/>
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59 <param help="(-type) " label="The kind of internal calibration that should be applied" name="param_type" optional="True" type="select" value="spectrumwise">
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60 <option value="spectrumwise">spectrumwise</option>
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61 <option value="global">global</option>
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62 </param>
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63 <param help="(-mz_tolerance) " label="Allowed tolerance between peak and reference m/z" min="0.0" name="param_algorithm_mz_tolerance" optional="True" type="float" value="1.0"/>
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64 <param help="(-mz_tolerance_unit) " label="Unit for mz_tolerance" name="param_algorithm_mz_tolerance_unit" optional="True" type="select" value="Da">
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65 <option value="Da">Da</option>
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66 <option value="ppm">ppm</option>
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67 </param>
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68 <param help="(-rt_tolerance) " label="Allowed tolerance between peak and reference rt" name="param_algorithm_rt_tolerance" type="integer" value="10"/>
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69 <expand macro="advanced_options">
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70 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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71 </expand>
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72 </inputs>
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73 <outputs>
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74 <data format="input" metadata_source="param_in" name="param_out"/>
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75 <data format="trafoxml" name="param_trafo"/>
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76 </outputs>
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77 <help>Applies an internal calibration.
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78
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79
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80 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html</help>
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81 </tool>