Mercurial > repos > ethevenot > profia
annotate profia_config.xml @ 2:3f8ae071bdda draft
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
author | ethevenot |
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date | Mon, 22 Jan 2018 11:32:41 -0500 |
parents | 4753e64cf694 |
children | de9d1270a9ae |
rev | line source |
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2
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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1 <tool id="profia" name="proFIA" version="3.1.0"> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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2 <description>Preprocessing of FIA-HRMS data</description> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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3 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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4 <requirements> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5 <requirement type="package">r-batch</requirement> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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6 <requirement type="package">bioconductor-proFIA</requirement> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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7 </requirements> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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8 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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9 <stdio> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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10 <exit_code range="1:" level="fatal" /> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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11 </stdio> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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12 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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13 <command> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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14 Rscript $__tool_directory__/profia_wrapper.R |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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15 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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16 #if $inputs.input == "lib": |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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17 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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18 #elif $inputs.input == "zip_file": |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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19 zipfile $inputs.zip_file |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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20 #end if |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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21 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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22 ppmN "$ppmN" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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23 dmzN "$dmzN" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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24 ppmGroupN "$ppmGroupN" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents:
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25 dmzGroupN "$dmzGroupN" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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26 fracGroupN "$fracGroupN" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents:
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27 imputeC "$imputeC" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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28 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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29 #if $advCpt.opcC == "full" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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30 bandCoverageN "$advCpt.bandCoverageN" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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31 sizeMinN "$advCpt.sizeMinN" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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32 scanMinI "$advCpt.scanMinI" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents:
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33 scanMaxI "$advCpt.scanMaxI" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents:
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34 #end if |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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35 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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36 dataMatrix_out "$dataMatrix_out" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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37 sampleMetadata_out "$sampleMetadata_out" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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38 variableMetadata_out "$variableMetadata_out" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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39 figure "$figure" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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40 information "$information" |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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41 </command> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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42 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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43 <inputs> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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44 <conditional name="inputs"> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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45 <param name="input" type="select" label="Choose your input method" > |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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46 <option value="zip_file" selected="true">Zip file from your history containing your raw files</option> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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47 <option value="lib" >Library directory name</option> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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48 </param> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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49 <when value="zip_file"> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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50 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file (see the details for file upload in the help section below)" /> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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51 </when> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents:
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52 <when value="lib"> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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53 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" > |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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54 <validator type="empty_field"/> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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55 </param> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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56 </when> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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57 </conditional> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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58 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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59 <param name="ppmN" label="Maximum deviation between centroids during band detection (in ppm)" type="text" value = "7" help="[ppm]" /> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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60 <param name="dmzN" label="Minimal maximum deviation between centroids during band detection (in Da)" type="text" value = "0.001" help="[dmz] shloud be at most 0.002 for high resolution" /> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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61 <param name="ppmGroupN" label="Accuracy of the mass spectrometer to be used during feature alignment (in ppm)" type="text" value = "3" help="[ppmGroup] Should be inferior to the ppm parameter above." /> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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62 <param name="dmzGroupN" label="Minimal accuracy of the mass spectrometer to be used during feature alignment (in Da)" type="text" value = "0.0005" help="[dmzGroup] shloud be at most 0.002 for high resolution" /> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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63 <param name="fracGroupN" label=" Minimum fraction of samples in which a peak should be detected in at least one class to be kept during feature alignment" type="text" value = "0.5" help="[fracGroup]" /> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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64 <param name="imputeC" label="Imputation method" type="select" help="[imputation]"> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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65 <option value="None">None</option> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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66 <option value="randomForest" selected="true">randomForest</option> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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67 </param> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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68 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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69 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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70 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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71 <conditional name="advCpt"> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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72 <param name="opcC" type="select" label="Advanced parameters" > |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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73 <option value="default" selected="true">Use default</option> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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74 <option value="full">Full parameter list</option> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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75 </param> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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76 <when value="default"/> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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77 <when value="full"> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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78 <param name="bandCoverageN" type="float" value="0.3" label="Minimum fraction of centroids in the estimated injection window for a band to be built" help="[bandCoverage] Must be between 0 and 1"/> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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79 <param name="sizeMinN" type="text" value="none" label="Minimum number of consecutive centroids for a band to be built" help="[sizeMin] If set to 'none', the half of the estimated injection window will be used"/> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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80 <param name="scanMinI" type="integer" value="1" label="First scan to be preprocessed" help="[scanMin]"/> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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81 <param name="scanMaxI" type="text" value="none" label="Last scan to be preprocessed" help="[scanMax] Set to 'none' to preprocess up to the last acquired scan"/> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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82 </when> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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83 </conditional> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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84 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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85 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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86 |
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87 </inputs> |
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88 |
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89 <outputs> |
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90 <data name="dataMatrix_out" label="${tool.name}_dataMatrix.tsv" format="tabular" ></data> |
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91 <data name="sampleMetadata_out" label="${tool.name}_sampleMetadata.tsv" format="tabular" ></data> |
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92 <data name="variableMetadata_out" label="${tool.name}_variableMetadata.tsv" format="tabular" ></data> |
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93 <data name="figure" label="${tool.name}_figure.pdf" format="pdf"/> |
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94 <data name="information" label="${tool.name}_information.txt" format="txt"/> |
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95 </outputs> |
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96 |
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97 <tests> |
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98 <test> |
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99 <param name="inputs|input" value="zip_file" /> |
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100 <param name="inputs|zip_file" value="input-plasFIA.zip" ftype="zip" /> |
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101 <param name="ppmN" value="2"/> |
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102 <param name="dmzN" value="0.0005"/> |
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103 <param name="ppmGroupN" value="1"/> |
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104 <param name="dmzGroupN" value="0.0005"/> |
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105 <param name="fracGroupN" value="0.1"/> |
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106 <param name="imputeC" value="randomForest"/> |
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107 <output name="dataMatrix_out" file="output-dataMatrix.tsv" /> |
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108 <output name="information"> |
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109 <assert_contents> |
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110 <has_text text="707 groups have been done" /> |
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111 <has_text text="3 samples x 707 variables" /> |
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112 <has_text text="2089 peaks detected" /> |
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113 </assert_contents> |
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114 </output> |
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115 </test> |
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116 </tests> |
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117 |
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118 <help> |
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119 |
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120 .. class:: infomark |
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121 |
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122 **Author** Alexis Delabriere and Etienne Thevenot (CEA, LIST, MetaboHUB Paris, etienne.thevenot@cea.fr) |
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123 |
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124 --------------------------------------------------- |
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125 |
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126 .. class:: infomark |
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127 |
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128 **Please cite** |
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129 |
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130 Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. (2017). *proFIA*: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *Bioinformatics*, **33**:3767-3775. `https://doi.org/10.1093/bioinformatics/btx458 <https://doi.org/10.1093/bioinformatics/btx458>`_ |
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131 |
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132 --------------------------------------------------- |
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133 |
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134 .. class:: infomark |
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135 |
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136 **R package** |
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137 |
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138 The **proFIA** package is available from the bioconductor repository `http://bioconductor.org/packages/proFIA <http://bioconductor.org/packages/proFIA>`_ |
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139 |
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140 --------------------------------------------------- |
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141 |
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142 .. class:: infomark |
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143 |
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144 **Tool updates** |
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145 |
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146 See the **NEWS** section at the bottom of this page |
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147 |
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148 --------------------------------------------------- |
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149 |
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150 ========================================================== |
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151 *proFIA*: A preprocessing workflow for FIA-HRMS data |
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152 ========================================================== |
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153 |
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154 ----------- |
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155 Description |
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156 ----------- |
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157 |
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158 **Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS)** is a promising approach for **high-throughput metabolomics** (Madalinski *et al.*, 2008; Fuhrer *et al.*, 2011; Draper *et al.*, 2013). FIA- HRMS data, however, cannot be preprocessed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. |
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159 |
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160 The **proFIA module is a workflow** allowing to preprocess FIA-HRMS raw data in **centroid** mode and open format (netCDF, mzData, mzXML, and mzML), and generates the table of peak intensities (**peak table**). The workflow consists in **peak detection and quantification** within individual sample files, followed by **alignment** between files in the m/z dimension, and **imputation** of the missing values in the final peak table (Delabriere *et al.*, submitted). For each ion, the graph representing the intensity as a function of time is called a **flowgram**. A flowgram can be modeled as I = kP + ME(P) + B + e, where k is the response factor (corresponding to the ionization properties of the analyte), P is the **sample peak** (normalized profile which is common for all analytes from a sample and depends on the flow injection conditions only), ME is the **matrix effect**, B is the **solvent baseline**, and e is the heteroscedastic noise. |
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161 |
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162 The generated peak table is available in the '3 table' W4M tabular format (**dataMatrix**, **sampleMetadata**, and **variableMetadata**) for downstream statistical analysis and annotation with W4M modules. |
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163 |
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164 A figure provides **diagnostics** and visualization of the preprocessed data set. |
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165 |
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166 --------------------------------------------------- |
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167 |
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168 .. class:: infomark |
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169 |
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170 **References** |
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171 |
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172 | Delabriere A., Hohenester U., Junot C. and Thevenot E.A. (2017). proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *Bioinformatics*, **33**:3767-3775. (https://doi.org/10.1093/bioinformatics/btx458) |
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173 | Draper J., Lloyd A., Goodacre R. and Beckmann M. (2013). Flow infusion electrospray ionisation mass spectrometry for high throughput, non-targeted metabolite fingerprinting: a review. *Metabolomics* 9, 4-29. (https://doi.org/10.1007/s11306-012-0449-x) |
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174 | Fuhrer T., Dominik H., Boris B. and Zamboni N. (2011). High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry. *Analytical Chemistry* 83, 7074-7080. (https://doi.org/10.1021/ac201267k) |
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175 | Madalinski G., Godat E., Alves S., Lesage D., Genin E., Levi P., Labarre J., Tabet J., Ezan E. and Junot, C. (2008). Direct introduction of biological samples into a LTQ-orbitrap hybrid mass spectrometer as a tool for fast metabolome analysis. *Analytical Chemistry* 80, 3291-3303. (https://doi.org/10.1021/ac7024915) |
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176 |
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177 --------------------------------------------------- |
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178 |
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179 ----------------- |
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180 Workflow position |
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181 ----------------- |
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182 |
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183 .. image:: profia_workflowPositionImage.png |
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184 :width: 600 |
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185 |
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186 ----------- |
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187 Input files |
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188 ----------- |
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189 |
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190 +---------------------------+------------+ |
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191 | Parameter : num + label | Format | |
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192 +===========================+============+ |
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193 | 1 : Choose your inputs | zip | |
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194 +---------------------------+------------+ |
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195 |
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196 --------------------------------------------------- |
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197 |
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198 .. class:: warningmark |
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199 |
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200 VERY IMPORTANT: Your data must be in **centroid** mode (centroidization of raw files and conversion to an open format can be achieved with the proteowizard software: http://proteowizard.sourceforge.net/). |
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201 |
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202 |
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203 You have two methods for your inputs: |
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204 | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories; see below). |
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205 | 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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206 |
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207 **Steps for creating the zip file** |
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208 |
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209 **Step1: Creating your directory and hierarchize the subdirectories** |
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210 |
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211 .. class:: warningmark |
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212 |
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213 VERY IMPORTANT: If you zip your files under Windows, you must use the **7Zip** software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug). |
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214 |
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215 1a) Prepare a parent folder with the name of your data set (e.g., 'arabidopsis') containing your files: |
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216 | 'arabidopsis/w1.raw' |
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217 | 'arabidopsis/w2.raw' |
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218 | ... |
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219 | 'arabidopsis/m1.raw' |
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220 | 'arabidopsis/m2.raw' |
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221 | ... |
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222 | |
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223 |
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224 1b) If you have several experimental conditions resulting in distinct profiles of your samples (e.g. 'wild-type' and 'mutant' genotypes), create subfolders for your files (e.g., 'wild' and 'mutant') into your parent folder: |
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225 | 'arabidopsis/wild/w1.raw' |
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226 | 'arabidopsis/wild/w2.raw' |
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227 | ... |
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228 | 'arabidopsis/mutant/m1.raw' |
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229 | 'arabidopsis/mutant/m2.raw' |
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230 | ... |
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231 | |
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232 |
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233 **Step2: Creating a zip file** |
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234 | Zip your **parent** folder (here the 'arabidopsis' folder) containing all the subfolders and files with **7Zip**. |
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235 | |
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236 |
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237 **Step 3 : Uploading it to our Galaxy server** |
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238 | If your zip file is less than 2Gb, you get use the **Upload File** tool and the **no_unzip.zip** type to upload it. |
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239 | Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf). |
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240 | For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org). |
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241 | |
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242 |
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243 ---------- |
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244 Parameters |
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245 ---------- |
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246 |
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247 Maximum deviation between centroids during band detection; in ppm (default = 7) |
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248 | m/z tolerance of centroids corresponding to the same ion from one scan to the other. |
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249 | |
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250 |
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251 Minimal maximum deviation between centroids during band detection; in Da (default = 0.001); to avoid bias at low mass values, the deviation is the maximum between this quantity and the deviation in ppm |
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252 | minimum m/z tolerance of centroids corresponding to the same ion from one scan to the other. |
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253 | |
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254 |
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255 Accuracy of the mass spectrometer to be used during feature alignment; in ppm (default = 3); should be less than the ppm parameter used for detection |
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256 | Should be inferior or equal to the ppm deviation parameter above. |
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257 | |
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258 |
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259 Minimal accuracy of the mass spectrometer to be used during feature alignment; in Da (default = 0.0005); to avoid bias at low mass values; the deviation is the maximum between this quantity and the deviation in ppm |
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260 | |
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261 |
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262 Minimum fraction of samples in which a peak should be detected in at least one class to be kept during feature alignment (default = 0.5) |
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263 | Identical to the corresponding parameter in XCMS. |
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264 | |
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265 |
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266 Imputation method for missing values (default = 'randomForest') |
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267 | |
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268 |
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269 Minimum fraction of centroids in the estimated injection window for a band to be built (advanced; default = 0.3) |
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270 | |
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271 |
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272 Minimum number of consecutive centroids for a band to be built (advanced; default = half of the size of the estimated injection window) |
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273 | |
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274 |
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275 First scan to be preprocessed (advanced; default = 1) |
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276 | |
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277 |
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278 Last scan to be preprocessed (advanced; default = last acquisition scan) |
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279 | |
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280 |
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281 ------------ |
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282 Output files |
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283 ------------ |
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284 |
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285 dataMatrix.tabular |
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286 | **dataMatrix** tabular separated file with the variables as rows and samples as columns. Missing values are indicated as 'NA' (i.e. when the signal was not significantly different from noise). |
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287 | |
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288 |
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289 sampleMetadata.tabular |
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290 | **sampleMetadata** tabular separated file containing the sample metadata as columns. |
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291 | |
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292 |
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293 variableMetadata.tabular |
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294 | **variableMetadata** tabular separated file containing the variable metadata as columns. The **timeShifted** flag is set to 1 when the flowgram is time shifted compared to the sample peak (probably due to liquid retention in the FI tube). The **corSampPeakMean** metric is the correlation between the feature flowgram and the sample peak (values are in [-1, 1]). A value below 0.2 suggests that the feature signal is affected by a strong matrix effect. The **meanSolvent** is the mean baseline signal in the feature flowgrams. The **signalOverSolventPvalueMean** is the mean p-value of the tests discriminating between signal and baseline solvent. |
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295 | |
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296 |
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297 figure.pdf |
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298 | Visualization and diagnostics about the preprocessed data set; **Feature quality**: Number of detected features per sample for each of the three categories: 'Well-behaved' features have a peak shape close to the sample peak (optimal FIA acquisition is achieved when the majority of the features fall into this category); 'Shifted' indicates a time shift compared to the sample peak, and probably results from retention in the FI tube; 'Significant Matrix Effect' corresponds to a correlation between the feature and the samples peaks of less than 0.2, which is usually caused by a strong matrix effect; **Sample peaks**: Visualization of the peak model for each sample; should have close shapes in case of similar FIA conditions; **m/z density**: may allow to detect a missing m/z value, and in turn, suggest that the *ppm* parameter should be modified; **PCA score plot** of the log10 intensities to detect sample outliers. |
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299 | |
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300 |
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301 information.txt |
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302 | Text file with all messages and warnings generated during the computation. |
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303 | |
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304 |
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305 --------------------------------------------------- |
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306 |
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307 --------------- |
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308 Working example |
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309 --------------- |
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310 |
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311 Figure output |
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312 ============= |
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313 |
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314 .. image:: profia_workingExampleImage.png |
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315 :width: 600 |
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316 |
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317 --------------------------------------------------- |
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318 |
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319 ---- |
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320 NEWS |
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321 ---- |
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322 |
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323 CHANGES IN VERSION 3.1.0 |
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324 ======================== |
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325 |
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326 NEW FEATURE |
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327 |
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328 randomForest method implemented for imputation of missing values |
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329 |
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330 CHANGES IN VERSION 3.0.6 |
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331 ======================== |
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332 |
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333 NEW FEATURE |
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334 |
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335 dmz (and dmzGroup) parameters added for the peak detection and grouping steps; bandCoverage, sizeMin, scanMin, and scanMax added as advanced parameters for peak detection |
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336 |
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337 |
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338 CHANGES IN VERSION 3.0.4 |
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339 ======================== |
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340 |
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341 MINOR MODIFICATION |
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342 |
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343 Details added in the documentation |
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344 |
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345 CHANGES IN VERSION 3.0.2 |
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346 ======================== |
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347 |
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348 NEW FEATURE |
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349 |
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350 Parallel processing |
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351 |
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352 |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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353 CHANGES IN VERSION 3.0.0 |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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354 ======================== |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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355 |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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356 NEW FEATURE |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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357 |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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358 Creation of the tool |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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359 |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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360 </help> |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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361 |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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362 <citations> |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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363 <citation type="doi">10.1093/bioinformatics/btx458</citation> |
3f8ae071bdda
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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364 <citation type="doi">10.1093/bioinformatics/btu813</citation> |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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365 </citations> |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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366 |
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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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367 </tool> |