Mercurial > repos > george-weingart > graphlan_import

comparison export2graphlan.xml @ 13:66c50eadf709 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author george-weingart
date Thu, 04 Sep 2014 14:20:17 -0400
parents 389074508060
children b084b394910e
comparison
equal deleted inserted replaced
12:389074508060 13:66c50eadf709
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 parameters7777 43 Input parameters8888
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.,
116 -i LEFSE_INPUT, --lefse_input LEFSE_INPUT 116 -i LEFSE_INPUT, --lefse_input LEFSE_INPUT
117 117
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
121 -t TREE, --tree TREE Output filename where save the input tree for GraPhlAn 122 -t TREE, --tree TREE Output filename where save the input tree for GraPhlAn
123
122 -a ANNOTATION, --annotation ANNOTATION : This is the Output filename where to save GraPhlAn annotation 124 -a ANNOTATION, --annotation ANNOTATION : This is the Output filename where to save GraPhlAn annotation
123 125
124 Input data matrix parameters: 126 Input data matrix parameters:
125 --sep SEP 127 --sep SEP
126 --out_table OUT_TABLE : This is where to write the processed data matrix to file 128 --out_table OUT_TABLE : This is where to write the processed data matrix to file