Mercurial > repos > marie-tremblay-metatoul > nmr_bucketing
annotate NmrBucketing_xml.xml @ 4:d61f6ceef5d6 draft
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
author | lecorguille |
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date | Tue, 22 Nov 2016 05:22:03 -0500 |
parents | 58679e85745f |
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rev | line source |
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4
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
changeset
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1 <tool id="NmrBucketing" name="NMR_Bucketing" version="1.0.3"> |
0
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
changeset
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2 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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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
parents:
diff
changeset
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4 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
changeset
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5 <requirements> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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6 <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
parents:
diff
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7 <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
parents:
diff
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8 </requirements> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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9 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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10 <stdio> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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11 <exit_code range="1:" level="fatal" /> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
changeset
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12 </stdio> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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13 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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14 <command> |
4
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
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15 Rscript '$__tool_directory__/NmrBucketing_wrapper.R' |
0
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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16 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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17 #if $inputs.input == "lib": |
4
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
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18 library '$__app__.config.user_library_import_dir/$__user_email__/$inputs.library' |
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
changeset
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19 #elif $inputs.input == "tsv_file": |
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
changeset
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20 tsvfile '$inputs.tsv_file' |
0
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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21 #elif $inputs.input == "zip_file": |
4
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
changeset
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22 zipfile '$inputs.zip_file' |
0
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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23 #end if |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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24 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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25 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
changeset
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26 ## Bucket width |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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27 bucket_width $bucket_width |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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28 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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29 ## Spectra borders |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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changeset
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30 left_border $left_border |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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31 right_border $right_border |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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32 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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33 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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34 ## Spectra representation |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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35 graphType $graphType |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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36 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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37 ## Exclusion zone |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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38 zone_exclusion_choices.choice ${zone_exclusion_choices.choice} |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
changeset
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39 #if str($zone_exclusion_choices.choice) == 'yes': |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
changeset
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40 #for $i in $zone_exclusion_choices.conditions: |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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41 zone_exclusion_left ${i.zone_exclusion_left} |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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42 zone_exclusion_right ${i.zone_exclusion_right} |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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43 #end for |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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44 #end if |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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45 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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46 ## Outputs |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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47 logOut log.log |
4
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
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48 dataMatrixOut '$dataMatrixOut' |
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
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49 sampleOut '$sampleOut' |
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
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50 variableOut '$variableOut' |
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
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51 graphOut '$graphOut'; cat log.log |
0
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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52 </command> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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53 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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54 <inputs> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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55 <conditional name="inputs"> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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56 <param name="input" type="select" label="Choose your inputs method" > |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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57 <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option> |
4
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
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58 <option value="tsv_file">Tsv file containing preprocessed spectra (from your history)</option> |
0
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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59 <option value="lib" >Library directory name</option> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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60 </param> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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61 <when value="zip_file"> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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62 <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
marie-tremblay-metatoul
parents:
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63 </when> |
4
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
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64 <when value="tsv_file"> |
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
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65 <param name="tsv_file" type="data" format="tabular" label="Tsv file" /> |
d61f6ceef5d6
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents:
3
diff
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66 </when> |
0
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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67 <when value="lib"> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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68 <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
marie-tremblay-metatoul
parents:
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69 <validator type="empty_field"/> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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70 </param> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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71 </when> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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72 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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73 </conditional> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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74 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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75 <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
marie-tremblay-metatoul
parents:
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76 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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77 <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
marie-tremblay-metatoul
parents:
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78 <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
marie-tremblay-metatoul
parents:
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79 |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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80 <conditional name="zone_exclusion_choices"> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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81 <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
marie-tremblay-metatoul
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82 <option value="yes" > yes </option> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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83 <option value="no" selected="true"> no </option> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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84 </param> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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85 <when value="yes"> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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86 <repeat name="conditions" title="exclusion zones"> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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87 <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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88 <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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89 </repeat> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff
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90 </when> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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91 <when value="no"> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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92 </when> |
a99a6026c972
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marie-tremblay-metatoul
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93 </conditional> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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94 |
a99a6026c972
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95 <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
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96 <option value="None"> none </option> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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97 <option value="Overlay"> Overlay </option> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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98 <option value="One_per_individual"> One_per_individual </option> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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99 </param> |
a99a6026c972
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100 |
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101 </inputs> |
a99a6026c972
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102 |
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103 <outputs> |
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104 <data format="tabular" name="sampleOut" label="${tool.name}_sampleMetadata" /> |
a99a6026c972
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105 <data format="tabular" name="variableOut" label="${tool.name}_variableMetadata" /> |
1
301d7adf862e
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106 <data format="tabular" name="dataMatrixOut" label="${tool.name}_bucketedData" /> |
0
a99a6026c972
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107 <data format="pdf" name="graphOut" label="${tool.name}_spectra" > |
a99a6026c972
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108 <filter> graphType != "None" </filter> |
a99a6026c972
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109 </data> |
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110 </outputs> |
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111 |
a99a6026c972
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112 <tests> |
a99a6026c972
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113 <test> |
a99a6026c972
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114 <param name="inputs|input" value="zip_file" /> |
a99a6026c972
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115 <param name="inputs|zip_file" value="MTBLS1.zip" ftype="zip" /> |
a99a6026c972
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116 <param name="bucket_width" value="0.01" ftype="zip" /> |
a99a6026c972
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117 <param name="left_border" value="9.3" /> |
a99a6026c972
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118 <param name="right_border" value="0.8" /> |
a99a6026c972
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119 <param name="zone_exclusion_choices|choice" value="yes" /> |
a99a6026c972
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120 <param name="zone_exclusion_choices|conditions_0|zone_exclusion_left" value="6.0" /> |
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121 <param name="zone_exclusion_choices|conditions_0|zone_exclusion_right" value="4.24" /> |
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122 <param name="zone_exclusion_choices|conditions_1|zone_exclusion_left" value="3.99" /> |
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planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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123 <param name="zone_exclusion_choices|conditions_1|zone_exclusion_right" value="3.19" /> |
a99a6026c972
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124 <param name="graphType" value="Overlay" /> |
a99a6026c972
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125 <output name="dataMatrixOut" file="MTBLS1_bucketedData.tabular" /> |
a99a6026c972
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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126 <output name="sampleOut" file="MTBLS1_sampleMetadata.tabular" /> |
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127 <output name="variableOut" file="MTBLS1_variableMetadata.tabular" /> |
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128 </test> |
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129 </tests> |
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130 |
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131 <help> |
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132 |
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133 .. class:: infomark |
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134 |
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135 **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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136 |
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137 |
a99a6026c972
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138 ============= |
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139 NMR Bucketing |
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140 ============= |
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141 |
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142 ----------- |
a99a6026c972
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143 Description |
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144 ----------- |
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145 |
a99a6026c972
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146 Bucketing / Binning (spectra segmentation in fixed-size windows) and integration (sum of absolute intensities inside each bucket) to preprocess NMR data |
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147 |
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148 ----------------- |
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149 Workflow position |
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150 ----------------- |
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151 |
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152 **Upstream tools** |
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153 |
4
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154 ========================= ============================ ======= |
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155 Name output file format |
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156 ========================= ============================ ======= |
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157 NMRAlignment NMR_Alignment_alignedSpectra tsv |
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158 ========================= ============================ ======= |
0
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159 |
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160 **Downstream tools** |
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161 |
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162 +---------------------------+----------------------+--------+ |
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163 | Name | Output file | Format | |
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164 +===========================+======================+========+ |
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165 |NmrNormalization | dataMatrix.tsv | Tabular| |
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166 +---------------------------+----------------------+--------+ |
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167 |Univariate | variableMetadata.tsv | Tabular| |
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168 +---------------------------+----------------------+--------+ |
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169 |Multivariate | sampleMetadata.tsv | Tabular| |
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170 +---------------------------+----------------------+--------+ |
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171 | | variableMetadata.tsv | Tabular| |
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172 +---------------------------+----------------------+--------+ |
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173 |
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174 |
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175 ----------- |
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176 Input files |
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177 ----------- |
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178 |
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179 +---------------------------+------------+ |
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180 | Parameter : num + label | Format | |
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181 +===========================+============+ |
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182 | 1 : Choose your inputs | zip | |
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183 +---------------------------+------------+ |
4
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184 | 1 : Choose your inputs | tsv | |
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185 +---------------------------+------------+ |
0
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186 |
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187 **Choose your inputs** |
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188 |
4
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189 You have three methods for your inputs: |
0
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190 |
4
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191 | Zip file (recommended): You can put a zip file containing your inputs as raw Bruker files: myinputs.zip (containing all your conditions as sub-directories). |
0
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192 | 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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193 | Tsv file: You can put a tsv file containing your inputs as preprocessed spectra: myinputs.tsv (containing all your conditions in columns and chemical shifts in rows). |
0
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194 |
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195 .. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png |
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196 :width: 800 |
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197 |
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198 ---------- |
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199 Parameters |
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200 ---------- |
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201 |
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202 Bucket width |
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203 | size of windows |
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204 | |
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205 |
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206 Left limit |
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207 | Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm |
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208 | |
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209 |
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210 Right limit |
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211 | Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm |
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212 | |
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213 |
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214 Exclusion zone(s) |
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215 | Spectral regions to exclude, water, solvents, ... resonance |
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216 | If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible, |
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217 | If NO: no zone to exclude |
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218 | Default value is NO |
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219 | |
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220 |
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221 Left exclusion zone |
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222 | Upper boundary of exclusion zone |
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223 | |
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224 |
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225 Right exclusion zone |
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226 | Lower boundary of exclusion zone |
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227 |
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228 | *Notes:* |
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229 | - these parameters can be used several times using the "Add new exclusion zones" button |
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230 | |
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231 |
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232 Spectra representation: |
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233 | Graphical chart of bucketed and integrated raw files |
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234 | If "Overlay": the n (sample number) spectra are overlaid on the same figure |
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235 | If "One_per_individual": pdf file includes n pages (1 per sample) |
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236 | |
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237 |
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238 |
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239 ------------ |
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240 Output files |
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241 ------------ |
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242 |
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243 |
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244 bucketedData.tsv |
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245 | tabular output |
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246 | Data matrix with p rows (buckets) and n columns (samples) containing the intensities |
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247 | |
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248 |
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249 sampleMetadata.tsv |
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250 | tabular output |
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251 | 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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252 | |
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253 |
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254 variableMetadata.tsv |
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255 | tabular output |
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256 | 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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257 | |
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258 |
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259 spectra.pdf |
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260 | pdf output |
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261 | Graphical chart of bucketed and integrated data |
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262 | |
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263 |
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264 |
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265 --------------------------------------------------- |
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266 |
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267 --------------- |
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268 Working example |
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269 --------------- |
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270 |
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271 |
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272 .. class:: warningmark |
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273 |
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274 Under construction |
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275 |
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276 .. image:: ./static/images/Mth_Travaux.png |
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277 :width: 100 |
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278 |
3
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279 --------------------------------------------------- |
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280 |
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281 Changelog/News |
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282 -------------- |
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283 |
4
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284 **Version 1.0.3 - 24/10/2016** |
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285 |
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286 - ENHANCEMENT: add possibility of bucketing processed files (upstream tools) |
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287 |
3
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288 **Version 1.0.2 - 12/08/2016** |
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289 |
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290 - ENHANCEMENT: x-axis customization: add chemical shift labels |
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291 |
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292 **Version 1.0.1 - 04/04/2016** |
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293 |
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294 - TEST: refactoring to pass planemo test using conda dependencies |
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295 |
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296 |
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297 **Version 2015-01-08 - 08/01/2015** |
0
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298 |
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299 </help> |
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300 <citations> |
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301 <citation type="doi">10.1093/bioinformatics/btu813</citation> |
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302 </citations> |
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303 </tool> |
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304 |