Mercurial > repos > george-weingart > graphlan_import

comparison export2graphlan.xml @ 11:8cfabe8759ab draft

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author george-weingart
date Thu, 04 Sep 2014 14:16:14 -0400
parents 733dfa77c6de
children 389074508060
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10:733dfa77c6de 11:8cfabe8759ab
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 parameters5555 43 Input parameters6666
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.,
122 -a ANNOTATION, --annotation ANNOTATION : This is the Output filename where to save GraPhlAn annotation 122 -a ANNOTATION, --annotation ANNOTATION : This is the Output filename where to save GraPhlAn annotation
123 123
124 Input data matrix parameters: 124 Input data matrix parameters:
125 --sep SEP 125 --sep SEP
126 --out_table OUT_TABLE : This is where to write the processed data matrix to file 126 --out_table OUT_TABLE : This is where to write the processed data matrix to file
127 --fname_row FNAME_ROW : Row number containing the names of the features 127 --fname_row FNAME_ROW : Row number containing the names of the features (default 0, specify -1 if no names are present in the matrix)
128 [default 0, specify -1 if no names are present in the
129 matrix
130 --sname_row SNAME_ROW 128 --sname_row SNAME_ROW
131 column number containing the names of the samples 129 column number containing the names of the samples (default 0, specify -1 if no names are present in the matrix)
132 [default 0, specify -1 if no names are present in the
133 matrix
134 --metadata_rows METADATA_ROWS 130 --metadata_rows METADATA_ROWS
135 Row numbers to use as metadata[default None, meaning 131 Row numbers to use as metadata[default None, meaning
136 no metadata 132 no metadata
137 --skip_rows SKIP_ROWS 133 --skip_rows SKIP_ROWS
138 Row numbers to skip (0-indexed, comma separated) from 134 Row numbers to skip (0-indexed, comma separated) from