Description

Compute the TCS score for a MSA or for a MSA plus a library file. Outputs the tcs as it is and a csv with just the total TCS score.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, … ]

msa:file

fasta file containing the alignment to be evaluated. May be gzipped or uncompressed.

*.{aln,fa,fasta,fas}{.gz,}

meta2:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

lib:file

lib file containing the alignment library of the given msa.

*{.tc_lib,*_lib}

Output

name:type
description
pattern

tcs

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.tcs:file

The msa represented in tcs format, prepended with TCS scores

*.tcs

scores

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.scores:file

a file containing the score of the alignment in csv format

*.scores

versions

versions.yml:file

File containing software versions

versions.yml

Tools

pigz

Parallel implementation of the gzip algorithm.

zlib.net/pigz zlib.net/pigz/pigz.pdf
included in
multiplesequencealign
maintainer
Github user alessiovignoli
get in touch
Ask a question on Slack Open an issue on GitHub