Groovy Map containing sample information
e.g. [ id:'test']
fasta (file)
Input sequences in FASTA format
*.{fa,fasta}
meta2 (map)
Groovy Map containing tree information
e.g. [ id:'test_tree']
tree (file)
Input guide tree in Newick format
*.{dnd}
meta3 (map)
Groovy Map containing tree information
e.g. [ id:'test_infos']
template (file)
T_coffee template file that maps sequences to the accessory information files to be used.
*
accessory_informations (file)
Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures.
*
compress (boolean)
Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded.
Output
Name (Type)
Description
Pattern
meta (map)
Groovy Map containing sample information
e.g. [ id:'test']
alignment (file)
Alignment file in FASTA format. May be gzipped.
*.aln{.gz,}
lib (file)
optional output, the library generated from the MSA file.
