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annotate runit/output/information.txt @ 2:596320b84315 draft

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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
author ethevenot
date Thu, 11 Jan 2018 12:52:08 -0500
parents b4f5b5bc01dd
children
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
ethevenot
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
ethevenot
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2 Start of the 'Quality Metrics' Galaxy module call: Thu 11 Jan 2018 06:23:47 PM
0
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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5 Data description:
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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7 observations: 9
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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8 variables: 10
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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9 missing: 12
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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10 0 values (%): 0
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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11 min: 4.04
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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12 mean: 1.1e+08
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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13 median: 3300
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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14 max: 1.5e+09
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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16 Sample types:
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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18 blank pool sample
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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19 2 2 5
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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22 Variables: Blank mean, sd, and CV
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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24 Variables: Sample mean, sd, and CV
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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26 Variables: Blank mean over sample mean
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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28 Variables: Pool mean, sd, and CV
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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30 Variables: Pool CV over sample CV
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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32 Observations: Hotelling ellipse
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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34 Observations: Missing values
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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36 Observations: Profile deciles
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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38 Plotting
2
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
ethevenot
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40 End of 'Quality Metrics' Galaxy module call: 2018-01-11 18:23:47
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
ethevenot
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44 ============================================================================
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
ethevenot
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45 Additional information about the call:
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
ethevenot
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47 1) Parameters:
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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48 $dataMatrix_in
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
ethevenot
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49 [1] "./input/dataMatrix.tsv"
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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51 $sampleMetadata_in
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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52 [1] "./input/sampleMetadata.tsv"
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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54 $variableMetadata_in
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
ethevenot
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55 [1] "./input/variableMetadata.tsv"
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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57 $sampleMetadata_out
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
ethevenot
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58 [1] "./output/sampleMetadata.tsv"
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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60 $variableMetadata_out
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
ethevenot
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61 [1] "./output/variableMetadata.tsv"
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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63 $figure
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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64 [1] "./output/figure.pdf"
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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66 $information
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
ethevenot
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67 [1] "./output/information.txt"
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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69 $CV
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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70 [1] "FALSE"
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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72 $Compa
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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73 [1] TRUE
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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74
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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75 $seuil
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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76 [1] 1
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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78 $poolAsPool1L
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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79 [1] TRUE
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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82 2) Session Info:
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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83 R version 3.3.1 (2016-06-21)
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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84 Main packages:
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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85 ropls 1.6.2 batch 1.1.4
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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86 Other loaded packages:
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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87 parallel 3.3.1 Biobase 2.34.0 methods 3.3.1 BiocGenerics 0.20.0
596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
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88 ============================================================================