Mercurial > repos > marie-tremblay-metatoul > nmr_bucketing

annotate NmrBucketing_xml.xml @ 3:58679e85745f draft

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 7cd224b2cbddcb2535640a3f76194bd235acb602-dirty
author lecorguille
date Fri, 12 Aug 2016 05:47:27 -0400
parents 301d7adf862e
children d61f6ceef5d6
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58679e85745f planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 7cd224b2cbddcb2535640a3f76194bd235acb602-dirty
lecorguille
parents: 1
diff changeset
1 <tool id="NmrBucketing" name="NMR_Bucketing" version="1.0.2">
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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3 <description> Bucketing and integration of NMR Bruker raw data</description>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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5 <requirements>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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6 <requirement type="package" version="3.1.2">R</requirement>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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7 <requirement type="package" version="1.1_4">r-batch</requirement>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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8 <requirement type="package" version="1.8.8">r-pracma</requirement>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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9 </requirements>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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11 <stdio>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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12 <exit_code range="1:" level="fatal" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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13 </stdio>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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14
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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15 <command>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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16 Rscript $__tool_directory__/NmrBucketing_wrapper.R
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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18 #if $inputs.input == "lib":
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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19 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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20 #elif $inputs.input == "zip_file":
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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21 zipfile $inputs.zip_file
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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22 #end if
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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25 ## Bucket width
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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26 bucket_width $bucket_width
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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27
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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28 ## Spectra borders
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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29 left_border $left_border
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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30 right_border $right_border
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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33 ## Spectra representation
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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34 graphType $graphType
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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35
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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36 ## Exclusion zone
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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37 zone_exclusion_choices.choice ${zone_exclusion_choices.choice}
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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38 #if str($zone_exclusion_choices.choice) == 'yes':
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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39 #for $i in $zone_exclusion_choices.conditions:
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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40 zone_exclusion_left ${i.zone_exclusion_left}
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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41 zone_exclusion_right ${i.zone_exclusion_right}
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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42 #end for
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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43 #end if
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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44
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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45 ## Outputs
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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46 logOut log.log
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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47 dataMatrixOut $dataMatrixOut
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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48 sampleOut $sampleOut
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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49 variableOut $variableOut
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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50 graphOut $graphOut; cat log.log
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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51 </command>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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52
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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53 <inputs>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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54 <conditional name="inputs">
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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55 <param name="input" type="select" label="Choose your inputs method" >
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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56 <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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57 <option value="lib" >Library directory name</option>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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58 </param>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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59 <when value="zip_file">
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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60 <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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61 </when>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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62 <when value="lib">
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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63 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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64 <validator type="empty_field"/>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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65 </param>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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66 </when>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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67
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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68 </conditional>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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69
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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70 <param name="bucket_width" label="Bucket width" type="float" value="0.04" help="Default value is 0.04 ppm"/>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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71
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72 <param name="left_border" label="Left Border" type="float" value="10.0" size="10" help="Default value is 10 ppm"/>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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73 <param name="right_border" label="Right Border" type="float" value="0.5" size="10" help="Default value is 0.5 ppm"/>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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74
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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75 <conditional name="zone_exclusion_choices">
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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76 <param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" >
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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77 <option value="yes" > yes </option>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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78 <option value="no" selected="true"> no </option>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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79 </param>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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80 <when value="yes">
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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81 <repeat name="conditions" title="exclusion zones">
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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82 <param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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83 <param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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84 </repeat>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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85 </when>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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86 <when value="no">
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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87 </when>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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diff changeset
88 </conditional>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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89
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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90 <param name="graphType" label="Spectra representation" type="select" help="Select 'None' for no representation,'Overlay' to overlay all spectra on a unique chart and 'One per individual' to generate an individual chart for each observation">
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
91 <option value="None"> none </option>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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92 <option value="Overlay"> Overlay </option>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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93 <option value="One_per_individual"> One_per_individual </option>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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diff changeset
94 </param>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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95
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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96 </inputs>
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97
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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98 <outputs>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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99 <data format="tabular" name="sampleOut" label="${tool.name}_sampleMetadata" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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100 <data format="tabular" name="variableOut" label="${tool.name}_variableMetadata" />
1
301d7adf862e planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit df8740e6849320412c96468d3c99830b25b9f0d6
lecorguille
parents: 0
diff changeset
101 <data format="tabular" name="dataMatrixOut" label="${tool.name}_bucketedData" />
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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102 <data format="pdf" name="graphOut" label="${tool.name}_spectra" >
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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103 <filter> graphType != "None" </filter>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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104 </data>
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marie-tremblay-metatoul
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105 </outputs>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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106
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107
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108 <tests>
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109 <test>
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110 <param name="inputs|input" value="zip_file" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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111 <param name="inputs|zip_file" value="MTBLS1.zip" ftype="zip" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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112 <param name="bucket_width" value="0.01" ftype="zip" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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113 <param name="left_border" value="9.3" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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114 <param name="right_border" value="0.8" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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115 <param name="zone_exclusion_choices|choice" value="yes" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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116 <param name="zone_exclusion_choices|conditions_0|zone_exclusion_left" value="6.0" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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117 <param name="zone_exclusion_choices|conditions_0|zone_exclusion_right" value="4.24" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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118 <param name="zone_exclusion_choices|conditions_1|zone_exclusion_left" value="3.99" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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119 <param name="zone_exclusion_choices|conditions_1|zone_exclusion_right" value="3.19" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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120 <param name="graphType" value="Overlay" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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121 <output name="dataMatrixOut" file="MTBLS1_bucketedData.tabular" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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122 <output name="sampleOut" file="MTBLS1_sampleMetadata.tabular" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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123 <output name="variableOut" file="MTBLS1_variableMetadata.tabular" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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124 </test>
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125 </tests>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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126
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marie-tremblay-metatoul
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127 <help>
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128
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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129 .. class:: infomark
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130
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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131 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr), Marion Landi (marion.landi@clermont.inra.fr) and Franck Giacomoni (fgiacomoni@clermont.inra.fr)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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132
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133
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marie-tremblay-metatoul
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134 =============
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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135 NMR Bucketing
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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136 =============
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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137
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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138 -----------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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139 Description
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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140 -----------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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141
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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142 Bucketing / Binning (spectra segmentation in fixed-size windows) and integration (sum of absolute intensities inside each bucket) to preprocess NMR data
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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143
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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144 -----------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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145 Workflow position
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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146 -----------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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147
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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148 **Upstream tools**
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149
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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150 ========================= ================= ======= =========
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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151 Name output file format parameter
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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152 ========================= ================= ======= =========
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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153 NA NA zip NA
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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154 ========================= ================= ======= =========
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155
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156
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157 **Downstream tools**
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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158
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159 +---------------------------+----------------------+--------+
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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160 | Name | Output file | Format |
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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161 +===========================+======================+========+
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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162 |NmrNormalization | dataMatrix.tsv | Tabular|
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marie-tremblay-metatoul
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163 +---------------------------+----------------------+--------+
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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164 |Univariate | variableMetadata.tsv | Tabular|
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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165 +---------------------------+----------------------+--------+
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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166 |Multivariate | sampleMetadata.tsv | Tabular|
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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167 +---------------------------+----------------------+--------+
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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168 | | variableMetadata.tsv | Tabular|
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marie-tremblay-metatoul
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169 +---------------------------+----------------------+--------+
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170
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171
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172 -----------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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173 Input files
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174 -----------
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175
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176 +---------------------------+------------+
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177 | Parameter : num + label | Format |
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178 +===========================+============+
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179 | 1 : Choose your inputs | zip |
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180 +---------------------------+------------+
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181
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182 **Choose your inputs**
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183
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184 You have two methods for your inputs:
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185
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186 | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
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187 | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.
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188
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189 .. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png
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190 :width: 800
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191
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192 ----------
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193 Parameters
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194 ----------
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195
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196 Bucket width
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197 | size of windows
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198 |
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199
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200 Left limit
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201 | Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm
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202 |
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203
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204 Right limit
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205 | Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm
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206 |
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207
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208 Exclusion zone(s)
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209 | Spectral regions to exclude, water, solvents, ... resonance
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210 | If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,
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211 | If NO: no zone to exclude
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212 | Default value is NO
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213 |
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214
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215 Left exclusion zone
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216 | Upper boundary of exclusion zone
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217 |
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218
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219 Right exclusion zone
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220 | Lower boundary of exclusion zone
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221
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222 | *Notes:*
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223 | - these parameters can be used several times using the "Add new exclusion zones" button
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224 |
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225
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226 Spectra representation:
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227 | Graphical chart of bucketed and integrated raw files
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228 | If "Overlay": the n (sample number) spectra are overlaid on the same figure
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229 | If "One_per_individual": pdf file includes n pages (1 per sample)
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230 |
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231
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232
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233 ------------
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234 Output files
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235 ------------
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236
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237
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238 bucketedData.tsv
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239 | tabular output
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240 | Data matrix with p rows (buckets) and n columns (samples) containing the intensities
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241 |
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242
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243 sampleMetadata.tsv
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244 | tabular output
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245 | file with n rows (samples) and 2 columns containing sample identifier (rownames) and sample order: the rownames of sampleMetadata must be identical to the colnames of the bucketedData. Can add columns with numeric and/or character sample metadata. This file is optional in the normalization step and mandatory in the statistical analysis step of the workflow.
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246 |
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247
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248 variableMetadata.tsv
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249 | tabular output
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250 | file with p rows (buckets) and 2 columns containing variable identifier (rownames) and bucket order: the rownames of variableMetadata must be identical to the rownames of the bucketedData. Can add columns with numeric and/or character variable metadata. This file is mandatory in the statistical analysis step of the workflow.
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251 |
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252
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253 spectra.pdf
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254 | pdf output
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255 | Graphical chart of bucketed and integrated data
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256 |
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257
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258
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259 ---------------------------------------------------
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260
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261 ---------------
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262 Working example
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263 ---------------
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264
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265
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266 .. class:: warningmark
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267
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268 Under construction
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269
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270 .. image:: ./static/images/Mth_Travaux.png
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271 :width: 100
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272
3
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273 ---------------------------------------------------
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274
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275 Changelog/News
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276 --------------
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277
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278 **Version 1.0.2 - 12/08/2016**
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279
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280 - ENHANCEMENT: x-axis customization: add chemical shift labels
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281
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282 **Version 1.0.1 - 04/04/2016**
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283
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284 - TEST: refactoring to pass planemo test using conda dependencies
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285
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286
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287 **Version 2015-01-08 - 08/01/2015**
0
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288
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289 </help>
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290 <citations>
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291 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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292 </citations>
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293 </tool>
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294