merge¶
Usage: taxpasta merge [OPTIONS] [PROFILE1 PROFILE2 [...]]
Standardise and merge two or more taxonomic profiles into a single table.
╭─ Arguments ────────────────────────────────────────────────────────────────────────────────╮
│ profiles [PROFILE1 PROFILE2 [...]] Two or more files containing taxonomic │
│ profiles. Required unless there is a sample │
│ sheet. Filenames will be parsed as sample │
│ names. │
╰────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ──────────────────────────────────────────────────────────────────────────────────╮
│ * --profiler -p [bracken|centrifuge|diam The taxonomic profiler │
│ ond|kaiju|kraken2|kraken used. All provided │
│ uniq|megan6|metaphlan|mo profiles must come from │
│ tus] the same tool! │
│ [required] │
│ --samplesheet -s FILE A table with a header and │
│ two columns: the first │
│ column named 'sample' │
│ which can be any string │
│ and the second column │
│ named 'profile' which │
│ must be a file path to an │
│ actual taxonomic │
│ abundance profile. If │
│ this option is provided, │
│ any arguments are │
│ ignored. │
│ [default: None] │
│ --samplesheet-format [TSV|CSV|ODS|XLSX|arrow| The file format of the │
│ parquet] sample sheet. Depending │
│ on the choice, additional │
│ package dependencies may │
│ apply. Will be parsed │
│ from the sample sheet │
│ file name but can be set │
│ explicitly. │
│ [default: None] │
│ * --output -o PATH The desired output file. │
│ By default, the file │
│ extension will be used to │
│ determine the output │
│ format. │
│ [required] │
│ --output-format [TSV|CSV|ODS|XLSX|arrow| The desired output │
│ parquet|BIOM] format. Depending on the │
│ choice, additional │
│ package dependencies may │
│ apply. Will be parsed │
│ from the output file name │
│ but can be set │
│ explicitly. │
│ [default: None] │
│ --wide --long Output merged abundance │
│ data in either wide or │
│ (tidy) long format. │
│ Ignored when the desired │
│ output format is BIOM. │
│ [default: wide] │
│ --help -h Show this message and │
│ exit. │
╰────────────────────────────────────────────────────────────────────────────────────────────╯