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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
author ethevenot
date Wed, 03 May 2017 10:49:08 -0400
parents 39ccace77270
children 3f8ae071bdda
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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4753e64cf694 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
ethevenot
parents: 0
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2 Start of the 'proFIA' Galaxy module call: Wed 03 May 2017 01:18:28 PM
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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3 files_root_directory plasFIA
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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5 1) Peak detection step ('proFIAset'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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7 2) Peak alignment ('group.FIA'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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4753e64cf694 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
ethevenot
parents: 0
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9 722 groups have been done .
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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11 3) Creating the peak table ('makeDataMatrix'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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13 4) Imputing missing values ('imputeMissingValues.WKNN_TN'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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15 5) Plotting ('plot'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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16 PCA
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4753e64cf694 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
ethevenot
parents: 0
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17 3 samples x 644 variables
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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18 standard scaling of predictors
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4753e64cf694 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
ethevenot
parents: 0
diff changeset
19 78 excluded variables (near zero variance)
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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20 R2X(cum) pre ort
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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21 Total 1 2 0
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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22 null device
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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23 1
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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25 6) Printing ('show'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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26 A "proFIAset" object containing 1 classes.
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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27 Missing values have been imputed.
1
4753e64cf694 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
ethevenot
parents: 0
diff changeset
28 2101 peaks detected.
4753e64cf694 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
ethevenot
parents: 0
diff changeset
29 722 features have been grouped.
0
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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30 The data matrix is avalaible.
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4753e64cf694 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
ethevenot
parents: 0
diff changeset
31 Memory usage: 0.419 MB
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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33 7) Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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34
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4753e64cf694 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
ethevenot
parents: 0
diff changeset
35 End of 'proFIA' Galaxy module call: 2017-05-03 13:27:09