Mercurial > repos > george-weingart > graphlan_import
comparison export2graphlan.xml @ 17:33a3a37c7872 draft
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| author | george-weingart |
|---|---|
| date | Thu, 04 Sep 2014 15:35:20 -0400 |
| parents | 8c34d0d94c44 |
| children | 51466b550e77 |
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| 16:8c34d0d94c44 | 17:33a3a37c7872 |
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| 8 -a $output_annot_file | 8 -a $output_annot_file |
| 9 --title $export_title | 9 --title $export_title |
| 10 --annotations $export_annotations | 10 --annotations $export_annotations |
| 11 --external_annotations $export_external_annotations | 11 --external_annotations $export_external_annotations |
| 12 --background_levels $background_levels | 12 --background_levels $background_levels |
| 13 #if $background_clades != " ": | 13 #if $str($background_clades) != " ": |
| 14 --background_clades $background_clades | 14 --background_clades $background_clades |
| 15 #end if | 15 #end if |
| 16 | 16 |
| 17 | 17 |
| 18 --skip_rows 1,2 | 18 --skip_rows 1,2 |
| 48 | 48 |
| 49 * **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. | 49 * **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. |
| 50 | 50 |
| 51 * **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. | 51 * **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. |
| 52 | 52 |
| 53 Input parameters1234 | 53 Input parameters5555 |
| 54 -------------------- | 54 -------------------- |
| 55 | 55 |
| 56 --annotations ANNOTATIONS | 56 --annotations ANNOTATIONS |
| 57 List which levels should be annotated in the tree. Use | 57 List which levels should be annotated in the tree. Use |
| 58 a comma separate values form, e.g., | 58 a comma separate values form, e.g., |