ma-export
Exports Kraken reports as MicrobiomeAnalyst-compatible files: counts.csv, taxonomy.csv, metadata.csv, and tree.nwk.
Syntax
kraut ma-export [OPTIONS] INPUT_FILES...
Arguments
| Argument |
Type |
Description |
INPUT_FILES... |
PATH |
Required. One or more Kraken report files. |
Options
| Option |
Short |
Type |
Description |
--outdir |
-o |
PATH |
Required. Output directory. |
--metadata |
|
PATH |
Optional metadata CSV or TSV file. |
--metadata-sample-col |
|
TEXT |
Column in the metadata matching input sample names. |
--pseudo-col |
|
TEXT |
Metadata column to create or overwrite with pseudo group labels (default: Random_label). |
--metric |
-m |
TEXT |
Count metric: LVL (taxon counts) or TOT (clade counts) (default: LVL). |
Example
kraut ma-export reports/*.krep -o ma_output
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