Mercurial > repos > george-weingart > graphlan_import
comparison export2graphlan.xml @ 5:32f1e56debb3 draft
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| author | george-weingart |
|---|---|
| date | Thu, 04 Sep 2014 13:58:56 -0400 |
| parents | c0c7f369e331 |
| children | 14edb544cdac |
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| 4:c0c7f369e331 | 5:32f1e56debb3 |
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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 parameters5678 |
| 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., |
| 112 the internal nodes | 112 the internal nodes |
| 113 | 113 |
| 114 input parameters: | 114 input parameters: |
| 115 You need to provide at least one of the two arguments | 115 You need to provide at least one of the two arguments |
| 116 -i LEFSE_INPUT, --lefse_input LEFSE_INPUT | 116 -i LEFSE_INPUT, --lefse_input LEFSE_INPUT |
| 117 LEfSe input data | 117 LEfSe input data |
| 118 | 118 |
| 119 -o LEFSE_OUTPUT, --lefse_output LEFSE_OUTPUT | 119 -o LEFSE_OUTPUT, --lefse_output LEFSE_OUTPUT |
| 120 LEfSe output result data | 120 LEfSe output result data |
| 121 | 121 |
| 122 output parameters: | 122 output parameters: |
| 123 -t TREE, --tree TREE Output filename where save the input tree for GraPhlAn | 123 -t TREE, --tree TREE Output filename where save the input tree for GraPhlAn |
| 124 -a ANNOTATION, --annotation ANNOTATION | 124 -a ANNOTATION, --annotation ANNOTATION |
| 125 Output filename where save GraPhlAn annotation | 125 Output filename where save GraPhlAn annotation |