Mercurial > repos > marie-tremblay-metatoul > 2dnmrannotation

annotate annotationRmn2D_xml.xml @ 4:cf11fa0c47c8 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
author workflow4metabolomics
date Thu, 23 Jan 2025 15:28:44 +0000
parents 546c7ccd2ed4
children
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4
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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1 <tool id="2DNmrAnnotation" name="2DNMRAnnotation" version="2.0.0+galaxy2" profile="20.09">
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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3 <description> Annotation of complex mixture bidimensional NMR spectra </description>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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4
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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5 <requirements>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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6 <requirement type="package" version="1.1_5">r-batch</requirement>
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7 <requirement type="package" version="0.8.3">r-dplyr</requirement>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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8 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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9 <requirement type="package" version="4.0.17">r-openxlsx</requirement>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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10 <requirement type="package" version="1.4.0">r-stringr</requirement>
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11 <requirement type="package" version="1.0.2">r-tidyr</requirement>
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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12 <requirement type="package" version="3.3">r-curl</requirement>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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13 <requirement type="package" version="1.6">r-jsonlite</requirement>
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cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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14 <requirement type="package" version="1">r-stringi</requirement>
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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15 </requirements>
4
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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16 <required_files>
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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17 <include path="annotationRmn2DWrapper.R" />
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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18 <include path="annotationRmn2D.R" />
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19 <include path="annotationRmn2DGlobale.R" />
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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20 <include path="viridis.R" />
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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21 <include path="BdDReference_COSY.RData" />
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22 <include path="BdDReference_HMBC.RData" />
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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23 <include path="BdDReference_HSQC.RData" />
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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24 <include path="BdDReference_JRES.RData" />
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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25 <include path="BdDReference_NOESY.RData" />
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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26 <include path="BdDReference_TOCSY.RData" />
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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27 </required_files>
2
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28 <stdio>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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29 <exit_code range="1:" level="fatal" />
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30 </stdio>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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31
4
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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32 <command detect_errors="aggressive"><![CDATA[
2
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33 ## Wrapper + Libraries of 2D-NMR sequences for reference compounds
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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34 Rscript '$__tool_directory__/annotationRmn2DWrapper.R'
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35
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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36 ## XLS file
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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37 xlsfile '$zip_xlsfile'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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38
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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39 ## Parameters to reduce search
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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40 pH $pH
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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41 magneticField $magneticField
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42
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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43 ## 2D-NMR sequences to annotate
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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44 cosy_2dsequences $cosy_2dsequences
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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45 jres_2dsequences $jres_2dsequences
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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46 hmbc_2dsequences $hmbc_2dsequences
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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47 hsqc_2dsequences $hsqc_2dsequences
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48 tocsy_2dsequences $tocsy_2dsequences
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49
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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50 ## In-house databases
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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51 inHouse_DB_choices.choice ${inHouse_DB_choices.choice}
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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52 #if str($inHouse_DB_choices.choice) == 'yes':
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53 inHouse_DB_cosy.choice ${inHouse_DB_choices.inHouse_DB_cosy.choice}
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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54 #if str($inHouse_DB_choices.inHouse_DB_cosy.choice) == 'yes':
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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55 cosyDB $inHouse_DB_choices.inHouse_DB_cosy.cosyDB
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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56 #end if
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57 inHouse_DB_hmbc.choice ${inHouse_DB_choices.inHouse_DB_hmbc.choice}
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58 #if str($inHouse_DB_choices.inHouse_DB_hmbc.choice) == 'yes':
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59 hmbcDB $inHouse_DB_choices.inHouse_DB_hmbc.hmbcDB
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60 #end if
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61 inHouse_DB_hsqc.choice ${inHouse_DB_choices.inHouse_DB_hsqc.choice}
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62 #if str($inHouse_DB_choices.inHouse_DB_hsqc.choice) == 'yes':
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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63 hsqcDB $inHouse_DB_choices.inHouse_DB_hsqc.hsqcDB
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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64 #end if
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65 inHouse_DB_jres.choice ${inHouse_DB_choices.inHouse_DB_jres.choice}
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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66 #if str($inHouse_DB_choices.inHouse_DB_jres.choice) == 'yes':
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67 jresDB $inHouse_DB_choices.inHouse_DB_jres.jresDB
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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68 #end if
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69 inHouse_DB_tocsy.choice ${inHouse_DB_choices.inHouse_DB_tocsy.choice}
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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70 #if str($inHouse_DB_choices.inHouse_DB_tocsy.choice) == 'yes':
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71 tocsyDB $inHouse_DB_choices.inHouse_DB_tocsy.tocsyDB
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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72 #end if
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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73 #end if
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74
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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75 ## Tolerances
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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76 tolppm1 $tolppm1
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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77 tolppm2 $tolppm2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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78 tolppmJRES $tolppmJRES
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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79
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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80 ## Treshold (probability score)
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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81 threshold $threshold
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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82
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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83 ## Unicity
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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84 unicity $unicity
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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85
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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diff changeset
86 ## Outputs
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
87 logOut '$logOut'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
88 annotationCOSY '$annotationCOSY'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
89 ppmCommunCOSY '$ppmCommunCOSY'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
90 annotationJRES '$annotationJRES'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
91 ppmCommunJRES '$ppmCommunJRES'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
92 annotationHMBC '$annotationHMBC'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
93 ppmCommunHMBC '$ppmCommunHMBC'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
94 annotationHSQC '$annotationHSQC'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
95 ppmCommunHSQC '$ppmCommunHSQC'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
96 annotationTOCSY '$annotationTOCSY'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
97 ppmCommunTOCSY '$ppmCommunTOCSY'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
98 annotationCombination '$annotationCombination'
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
99 AnnotationGraph '$AnnotationGraph'
4
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
workflow4metabolomics
parents: 3
diff changeset
100 ]]></command>
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
101
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
102 <inputs>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
103 <param name="zip_xlsfile" type="data" format="xlsx" label="File to annotate in xlsx format" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
104
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
diff changeset
105 <param name="pH" type="float" value="0" help="pH value of standards. Default value is 0 (no specific pH value required)" />
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
diff changeset
106 <param name="magneticField" type="integer" value="0" help="Magnetic filed of NMR spectrometer used to generate standard spectra. Default value is 0 (no specific field required)" />
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
diff changeset
107
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
108 <param name="cosy_2dsequences" type="select" label="2D-NMR COSY sequence">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
109 <option value="yes" > yes </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
110 <option value="no" selected="true"> no </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
111 </param>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
112 <param name="hmbc_2dsequences" type="select" label="2D-NMR HMBC sequence">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
113 <option value="yes" > yes </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
114 <option value="no" selected="true"> no </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
115 </param>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
116 <param name="hsqc_2dsequences" type="select" label="2D-NMR HSQC sequence">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
117 <option value="yes" > yes </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
118 <option value="no" selected="true"> no </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
119 </param>
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
diff changeset
120 <param name="jres_2dsequences" type="select" label="2D-NMR JRES sequence">
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
diff changeset
121 <option value="yes" > yes </option>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
diff changeset
122 <option value="no" selected="true"> no </option>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
diff changeset
123 </param>
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
124 <param name="tocsy_2dsequences" type="select" label="2D-NMR TOCSY sequence">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
125 <option value="yes" > yes </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
126 <option value="no" selected="true"> no </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
127 </param>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
128
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
129 <conditional name="inHouse_DB_choices">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
130 <param name="choice" type="select" label="In-house database" help="Choose if you want to use use in-house database to annotate" >
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
131 <option value="yes" > yes </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
132 <option value="no" selected="true"> no </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
133 </param>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
134 <when value="yes">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
135 <conditional name="inHouse_DB_cosy">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
136 <param name="choice" type="select" label="COSY In-house database" help="Choose if you want to use use in-house database to annotate COSY sequence" >
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
137 <option value="yes" > yes </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
138 <option value="no" selected="true"> no </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
139 </param>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
140 <when value="yes">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
141 <param name="cosyDB" type="data" format="no_unzip.zip" label="Zip file of the COSY RData object" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
142 </when>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
143 <when value="no" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
144 </conditional>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
145 <conditional name="inHouse_DB_hmbc">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
146 <param name="choice" type="select" label="HMBC In-house database" help="Choose if you want to use use in-house database to annotate HMBC sequence" >
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
147 <option value="yes" > yes </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
148 <option value="no" selected="true"> no </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
149 </param>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
150 <when value="yes">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
151 <param name="hmbcDB" type="data" format="no_unzip.zip" label="Zip file of the HMBC RData object" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
152 </when>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
153 <when value="no" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
154 </conditional>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
155 <conditional name="inHouse_DB_hsqc">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
156 <param name="choice" type="select" label="HSQC In-house database" help="Choose if you want to use use in-house database to annotate HSQC sequence" >
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
157 <option value="yes" > yes </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
158 <option value="no" selected="true"> no </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
159 </param>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
160 <when value="yes">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
161 <param name="hsqcDB" type="data" format="no_unzip.zip" label="Zip file of the HSQC RData object" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
162 </when>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
163 <when value="no" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
164 </conditional>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
165 <conditional name="inHouse_DB_jres">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
166 <param name="choice" type="select" label="JRES In-house database" help="Choose if you want to use use in-house database to annotate JRES sequence" >
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
167 <option value="yes" > yes </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
168 <option value="no" selected="true"> no </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
169 </param>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
170 <when value="yes">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
171 <param name="jresDB" type="data" format="no_unzip.zip" label="Zip file of the JRES RData object" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
172 </when>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
173 <when value="no" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
174 </conditional>
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175 <conditional name="inHouse_DB_tocsy">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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176 <param name="choice" type="select" label="TOCSY In-house database" help="Choose if you want to use use in-house database to annotate TOCSY sequence" >
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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177 <option value="yes" > yes </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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178 <option value="no" selected="true"> no </option>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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179 </param>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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180 <when value="yes">
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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181 <param name="tocsyDB" type="data" format="no_unzip.zip" label="Zip file of the TOCSY RData object" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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parents:
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182 </when>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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183 <when value="no" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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184 </conditional>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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185 </when>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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186 <when value="no" />
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187 </conditional>
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188
3
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189 <param name="tolppm1" type="float" min="0" value="0.01" help="Tolerance on chemical shift for the x-axis (H). Default value is 0.01ppm" />
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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parents: 2
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190 <param name="tolppm2" type="float" min="0" value="0.5" help="Tolerance on chemical shift for the y-axis (C). Default value is 0.01ppm" />
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
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191 <param name="tolppmJRES" type="float" min="0" value="0.002" help="Tolerance on chemical shift for the y-axis for the JRES sequence. Default value is 0.002 (Hz)" />
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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192
3
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parents: 2
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193 <param name="threshold" type="float" min="0" max="1" value="0" help="Treshold on score of presence. Default value is 0" />
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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194
3
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workflow4metabolomics
parents: 2
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195 <param name="unicity" label="Unicity of annotation" type="select" display="radio" help="Select only chemical shifts corresponding to one one metabolite">
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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196 <option value="no">No</option>
3
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parents: 2
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197 <option value="yes">Yes</option>
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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198 </param>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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199
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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diff changeset
200 </inputs>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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diff changeset
201
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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diff changeset
202 <outputs>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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203 <data format="txt" name="logOut" label="${tool.name}_log" />
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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parents: 2
diff changeset
204
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
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205 <data format="tabular" name="annotationCOSY" label="${tool.name}_annotationCOSY" >
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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206 <filter> cosy_2dsequences != "no" </filter>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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diff changeset
207 </data>
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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parents: 2
diff changeset
208 <data format="tabular" name="ppmCommunCOSY" label="${tool.name}_uplicateCOSY" >
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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diff changeset
209 <filter> cosy_2dsequences != "no" </filter>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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diff changeset
210 </data>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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211
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
parents: 2
diff changeset
212 <data format="tabular" name="annotationJRES" label="${tool.name}_annotationJRES" >
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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diff changeset
213 <filter> jres_2dsequences != "no" </filter>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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214 </data>
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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parents: 2
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215 <data format="tabular" name="ppmCommunJRES" label="${tool.name}_duplicateJRES" >
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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diff changeset
216 <filter> jres_2dsequences != "no" </filter>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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217 </data>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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218
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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parents: 2
diff changeset
219 <data format="tabular" name="annotationHMBC" label="${tool.name}_annotationHMBC" >
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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220 <filter> hmbc_2dsequences != "no" </filter>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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diff changeset
221 </data>
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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222 <data format="tabular" name="ppmCommunHMBC" label="${tool.name}_duplicateHMBC" >
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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diff changeset
223 <filter> hmbc_2dsequences != "no" </filter>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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diff changeset
224 </data>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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225
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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226 <data format="tabular" name="annotationHSQC" label="${tool.name}_annotationHSQC" >
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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diff changeset
227 <filter> hsqc_2dsequences != "no" </filter>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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228 </data>
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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229 <data format="tabular" name="ppmCommunHSQC" label="${tool.name}_duplicateHSQC" >
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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230 <filter> hsqc_2dsequences != "no" </filter>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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231 </data>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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232
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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233 <data format="tabular" name="annotationTOCSY" label="${tool.name}_annotationTOCSY" >
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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234 <filter> tocsy_2dsequences != "no" </filter>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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235 </data>
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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diff changeset
236 <data format="tabular" name="ppmCommunTOCSY" label="${tool.name}_duplicateTOCSY" >
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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diff changeset
237 <filter> tocsy_2dsequences != "no" </filter>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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238 </data>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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239
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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240 <data format="tabular" name="annotationCombination" label="${tool.name}_annotationCombination" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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241 <data format="pdf" name="AnnotationGraph" label="${tool.name}_graph" />
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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diff changeset
242 </outputs>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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diff changeset
243 <tests>
4
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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244 <test expect_num_outputs="13" expect_test_failure="true">
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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245 <param name="zip_xlsfile" value="Template_melange.xlsx" ftype="xlsx"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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246 <param name="cosy_2dsequences" value="yes"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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247 <param name="jres_2dsequences" value="yes"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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248 <param name="hmbc_2dsequences" value="yes"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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249 <param name="hsqc_2dsequences" value="yes"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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250 <param name="tocsy_2dsequences" value="yes"/>
4
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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diff changeset
251 <section name="inHouse_DB_choices">
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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252 <param name="choice" value="no"/>
cf11fa0c47c8 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
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253 </section>
3
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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diff changeset
254 <param name="tolppm1" value="0.01"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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255 <param name="tolppm2" value="0.5"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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256 <param name="tolppmJRES" value="0.002"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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257 <param name="threshold" value="0.3"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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258 <param name="unicity" value="no"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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259 <output name="annotationCOSY" file="2DNMRAnnotation_annotationCOSY.tabular"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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260 <output name="ppmCommunCOSY" file="2DNMRAnnotation_duplicateCOSY.tabular"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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261 <output name="annotationHMBC" file="2DNMRAnnotation_annotationHMBC.tabular"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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262 <output name="ppmCommunHMBC" file="2DNMRAnnotation_duplicateHMBC.tabular"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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263 <output name="annotationHSQC" file="2DNMRAnnotation_annotationHSQC.tabular"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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264 <output name="ppmCommunHSQC" file="2DNMRAnnotation_duplicateHSQC.tabular"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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265 <output name="annotationJRES" file="2DNMRAnnotation_annotationJRES.tabular"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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266 <output name="ppmCommunJRES" file="2DNMRAnnotation_duplicateJRES.tabular"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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267 <output name="annotationTOCSY" file="2DNMRAnnotation_annotationTOCSY.tabular"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
workflow4metabolomics
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268 <output name="ppmCommunTOCSY" file="2DNMRAnnotation_duplicateTOCSY.tabular"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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269 <output name="annotationCombination" file="2DNMRAnnotation_annotationCombination.tabular"/>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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270 </test>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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271 </tests>
546c7ccd2ed4 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
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272 <help>
2
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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273
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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274 .. class:: infomark
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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275
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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276 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@inra.fr), Coline Gardou
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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277
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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278 .. class:: infomark
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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279
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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280
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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281 ---------------------------------------------------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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282
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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283 ============================
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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284 Bidimensional NMR Annotation
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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285 ============================
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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286
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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287 -----------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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288 Description
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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289 -----------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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290
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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291 BARSA is an automatic algorithm for bi-dimensional NMR spectra annotation
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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292
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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293 -----------------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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294 Workflow position
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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295 -----------------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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296
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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297 **Upstream tools**
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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298
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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299 ========================= ================= ======= =========
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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300 Name output file format parameter
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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301 ========================= ================= ======= =========
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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302 NA NA NA NA
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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303 ========================= ================= ======= =========
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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304
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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305
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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306 **Downstream tools**
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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307
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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308 ========================= ================= ======= =========
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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309 Name output file format parameter
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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310 ========================= ================= ======= =========
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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311 NA NA NA NA
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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312 ========================= ================= ======= =========
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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313
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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314
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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315
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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316 -----------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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317 Input files
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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318 -----------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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319
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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320 +---------------------------+------------+
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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321 | Parameter : num + label | Format |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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322 +===========================+============+
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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323 | 1 : Choose your inputs | xlsx |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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324 +---------------------------+------------+
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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325
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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326 **Choose your inputs**
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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327 | xlsx file can include several peak lists, coming from several 2D NMR sequences
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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328 |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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329
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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330 .. image:: ./static/images/2DNmr_FileToAnnotate_xlsxFormat.png
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
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331
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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332 ----------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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diff changeset
333 Parameters
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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334 ----------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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335
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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336 Bi-dimensional NMR peak list(s) to annotate; select one or more sequence(s)
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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337 | COSY: yes/no
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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338 | JRES: yes/no
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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339 | HMBC: yes/no
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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diff changeset
340 | HSQC: yes/no
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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341 | TOCSY: yes/no
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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342 | Default value is no
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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343 |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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344
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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345 In-house databases
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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346 | Use of your own databases to annotate peak list(s)
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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347 | If YES: parameters **COSY In-house database**, **JRES In-house database**, ** HMBC In-house database**, **HSQC In-house database** and **TOCSY In-house database** are visible
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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348 | Select one or more in-house database
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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349 |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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350
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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351
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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diff changeset
352 Tolerances
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
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353 | tolppm1: Maximum variation of the chemical shift (due to experimental conditions) of a peak along the x-axis
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
354 | tolppm2: Maximum variation of the chemical shift (due to experimental conditions) of a peak along the y-axis
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
355 | tolppmJRES: Maximum variation of the chemical shift (due to experimental conditions) of a peak for the JRES sequence
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
356 | Default values: 0.01 and 0.01 ppm; 0.002 Hz
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
357 |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
358
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
359
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
360 Threshold
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
361 | All metabolites with a presence probability (number of detected peak(s)/number of theoretical peak(s)) under this threshold are removed
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
362 | Default value: 0
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
363 |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
364
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
365
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
366 Unicity of annotation
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
367 | All the peaks assigned to more than one metabolite are removed
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
368 |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
369
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
370
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
371 ------------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
372 Output files
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
373 ------------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
374 COSY
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
375 | tabular outputs
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
376 | annotationCOSY: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
377 | ppmCommunCOSY: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
378 | Only display if COSY was chosen
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
379 |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
380
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
381
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
382 JRES
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
383 | tabular outputs
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
384 | annotationJRES: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
385 | ppmCommunJRES: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
386 | Only display if JRES was chosen
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
387 |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
388
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
389
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
390 HMBC
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
391 | tabular outputs
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
392 | annotationHMBC: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
393 | ppmCommunHMBC: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
394 | Only display if HMBC was chosen
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
395 |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
396
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
397
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
398 HSQC
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
399 | tabular outputs
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
400 | annotationHSQC: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
401 | ppmCommunHSQC: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
402 | Only display if HSQC was chosen
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
403 |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
404
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
405
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
406 TOCSY
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
407 | tabular outputs
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
408 | annotationTOCSY: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
409 | ppmCommunTOCSY: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
410 | Only display if TOCSY was chosen
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
411 |
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
412
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
413
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
414 annotationCombination
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
415 | tabular outputs
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
416 | Array with p rows (corresponding to the identified metabolites) including the Metabolite name, the COSY presence probability, the JRES presence probability, the HMBC presence probability, the HSQC presence probability, the TOCSY presence probability and the averageScore
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
417 | Depends on the chosen sequences
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
418 | Only display if 2 or more sequences have be chosen
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
419
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
420
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
421 AnnotationGraph.pdf
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
422 | pdf output
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
423 | Bi-dimensional graphical chart of real pairs of chemical shifts, with name of identified metabolites
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
424
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
425
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
426
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
427 ---------------------------------------------------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
428
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
429 -------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
430 Example
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
431 -------
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
432 Example of output files obtaining wehn running the algorithm on a mix of 23 known compounds
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
433
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
434 .. image:: ./static/images/OutputsExampleMix.png
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
435 :width: 500
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
436
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
437 </help>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
438 <citations>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
439 <citation type="doi">10.1093/bioinformatics/btu813</citation>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
440 </citations>
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
441
dff7bde22102 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
workflow4metabolomics
parents:
diff changeset
442 </tool>