Mercurial > repos > george-weingart > graphlan_import

comparison export2graphlan.xml @ 3:ebe3cb467f8c draft

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author george-weingart
date Thu, 04 Sep 2014 13:51:33 -0400
parents dba11280df2c
children c0c7f369e331
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2:dba11280df2c 3:ebe3cb467f8c
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 parameters 43 Input parameters
44 ---------------- 44 ----------------
45 45
46 #
47 --annotations ANNOTATIONS 46 --annotations ANNOTATIONS
48 List which levels should be annotated in the tree. Use 47 List which levels should be annotated in the tree. Use
49 a comma separate values form, e.g., 48 a comma separate values form, e.g.,
50 --annotation_levels 1,2,3. Default is None 49 --annotation_levels 1,2,3. Default is None
51 --external_annotations EXTERNAL_ANNOTATIONS 50 --external_annotations EXTERNAL_ANNOTATIONS
112 values. Default behavior do not sum-up abundances on 111 values. Default behavior do not sum-up abundances on
113 the internal nodes 112 the internal nodes
114 113
115 input parameters: 114 input parameters:
116 You need to provide at least one of the two arguments 115 You need to provide at least one of the two arguments
117 -i LEFSE_INPUT, --lefse_input LEFSE_INPUT 116 -i LEFSE_INPUT, --lefse_input LEFSE_INPUT
118 LEfSe input data 117 LEfSe input data
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