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{:bash}

:map

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

msa{:bash}

:file

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

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

meta2{:bash}

:map

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

lib{:bash}

:file

lib file containing the alignment library of the given msa.

*{.tc_lib,*_lib}

Output

name:type
description
pattern

tcs{:bash}

meta{:bash}

:map

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

*.tcs{:bash}

:file

The msa represented in tcs format, prepended with TCS scores

*.tcs

scores{:bash}

meta{:bash}

:map

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

*.scores{:bash}

:file

a file containing the score of the alignment in csv format

*.scores

versions_tcoffee{:bash}

${task.process}{:bash}

:string

The name of the process

tcoffee{:bash}

:string

The name of the tool

t_coffee -version | awk '{gsub("Version_", ""); print \$3}'{:bash}

:eval

The expression to obtain the version of the tool

versions_pigz{:bash}

${task.process}{:bash}

:string

The name of the process

pigz{:bash}

:string

The name of the tool

pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

tcoffee{:bash}

:string

The name of the tool

t_coffee -version | awk '{gsub("Version_", ""); print \$3}'{:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

pigz{:bash}

:string

The name of the tool

pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//"{:bash}

:eval

The expression to obtain the version of the tool

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
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