Mercurial > repos > george-weingart > graphlan_import
comparison export2graphlan.xml @ 8:3fb300120fe1 draft
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| author | george-weingart |
|---|---|
| date | Thu, 04 Sep 2014 14:06:46 -0400 |
| parents | 09eff46a46e7 |
| children | cc25a2f6b1b9 |
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| 7:09eff46a46e7 | 8:3fb300120fe1 |
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| 38 | 38 |
| 39 * **Result of MetaPhlAn or HUMAnN analysis**: As depicted in the image below, this file can be the result of a MetaPhlAn analysis or a HUMAnN analysis. Generally, it is a tab separated file that have for each row a taxonomy and an abundance value. | 39 * **Result of MetaPhlAn or HUMAnN analysis**: As depicted in the image below, this file can be the result of a MetaPhlAn analysis or a HUMAnN analysis. Generally, it is a tab separated file that have for each row a taxonomy and an abundance value. |
| 40 | 40 |
| 41 * **Output of LEfSe**: This file is the result of LEfSe execute on the *Result of MetaPhlAn or HUMAnN analysis* file. This file allow GraPhlAn to highlight for you the found biomarkers. | 41 * **Output of LEfSe**: This file is the result of LEfSe execute on the *Result of MetaPhlAn or HUMAnN analysis* file. This file allow GraPhlAn to highlight for you the found biomarkers. |
| 42 | 42 |
| 43 Input parameters1234 | 43 Input parameters3333 |
| 44 -------------------- | 44 -------------------- |
| 45 | 45 |
| 46 --annotations ANNOTATIONS | 46 --annotations ANNOTATIONS |
| 47 List which levels should be annotated in the tree. Use | 47 List which levels should be annotated in the tree. Use |
| 48 a comma separate values form, e.g., | 48 a comma separate values form, e.g., |
| 118 -o LEFSE_OUTPUT, --lefse_output LEFSE_OUTPUT | 118 -o LEFSE_OUTPUT, --lefse_output LEFSE_OUTPUT |
| 119 | 119 |
| 120 output parameters: | 120 output parameters: |
| 121 -t TREE, --tree TREE Output filename where save the input tree for GraPhlAn | 121 -t TREE, --tree TREE Output filename where save the input tree for GraPhlAn |
| 122 -a ANNOTATION, --annotation ANNOTATION | 122 -a ANNOTATION, --annotation ANNOTATION |
| 123 Output filename where save GraPhlAn annotation | 123 Output filename where save GraPhlAn annotation |
| 124 | 124 |
| 125 Input data matrix parameters: | 125 Input data matrix parameters: |
| 126 --sep SEP | 126 --sep SEP |
| 127 --out_table OUT_TABLE | 127 --out_table OUT_TABLE |
| 128 Write processed data matrix to file | 128 Write processed data matrix to file |