Groovy Map containing sample information
e.g. [ id:'test']
fasta{:bash}
:file
Input sequences in FASTA format
*.{fa,fasta}
meta2{:bash}
:map
Groovy Map containing tree information
e.g. [ id:'test_tree']
tree{:bash}
:file
Input guide tree in Newick format
*.{dnd}
compress{:bash}
:boolean
Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is handled by passing ‘-gz’ to FAMSA along with any other options specified in task.ext.args.
Output
name:type
description
pattern
alignment{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test']
${prefix}.aln{.gz,}{:bash}
:file
Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false
*.aln{.gz,}
versions_famsa{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
famsa{:bash}
:string
The tool name
famsa -help 2>&1 | sed '2!d;s/ (.*//; s/^.* //'{: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
famsa{:bash}
:string
The name of the tool
famsa -help 2>&1 | sed '2!d;s/ (.*//; s/^.* //'{:bash}
:eval
The expression to obtain the version of the tool
Tools
famsa
GPL v3
Algorithm for large-scale multiple sequence alignments
