Mercurial > repos > george-weingart > graphlan_import

comparison export2graphlan.xml @ 9:cc25a2f6b1b9 draft

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author george-weingart
date Thu, 04 Sep 2014 14:09:50 -0400
parents 3fb300120fe1
children 733dfa77c6de
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8:3fb300120fe1 9:cc25a2f6b1b9
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.
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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.
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43 Input parameters3333 43 Input parameters4444
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.,
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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 : This is the Output filename where to save GraPhlAn annotation
123 Output filename where save GraPhlAn annotation
124 123
125 Input data matrix parameters: 124 Input data matrix parameters:
126 --sep SEP 125 --sep SEP
127 --out_table OUT_TABLE 126 --out_table OUT_TABLE : This is where to write the processed data matrix to file
128 Write processed data matrix to file
129 --fname_row FNAME_ROW 127 --fname_row FNAME_ROW
130 row number containing the names of the features 128 row number containing the names of the features
131 [default 0, specify -1 if no names are present in the 129 [default 0, specify -1 if no names are present in the
132 matrix 130 matrix
133 --sname_row SNAME_ROW 131 --sname_row SNAME_ROW