Multiple Sequence Alignment using Graph Clustering
Input
name:type
description
pattern
meta
:map
Groovy Map containing the fasta meta information
e.g. [ id:'test', single_end:false ]
fasta
:file
Input sequences in FASTA format.
*.{fa,fna,fasta}
meta2
:map
Groovy Map containing sample information for the specified guide tree (if supplied)
e.g. [ id:'test', single_end:false ]
tree
:file
Optional path to a file containing a guide tree in newick format to use as input. If empty, or overwritten by passing -t [fasttree|fasttree-noml|clustal|parttree], MAGUS will construct its own guide tree. If empty, fasttree is used as a default.
*.{dnd,tree}
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
alignment
meta
:map
Groovy Map containing sample meta information.
e.g. [ id:'test', single_end:false ]
*.aln{.gz,}
:file
File containing the output alignment, in FASTA format containing gaps. The sequences may be in a different order than in the input FASTA. The output file may or may not be gzipped, depending on the value supplied to compress.
*.aln{.gz,}
versions_magus
${task.process}
:string
The name of the process
magus
:string
The name of the tool
magus --version
:eval
The expression to obtain the version of the tool
versions_pigz
${task.process}
:string
The name of the process
pigz
:string
The name of the tool
pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//"
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
magus
:string
The name of the tool
magus --version
:eval
The expression to obtain the version of the tool
${task.process}
:string
The name of the process
pigz
:string
The name of the tool
pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//"
:eval
The expression to obtain the version of the tool
Tools
magus
MIT
Multiple Sequence Alignment using Graph Clustering
