Groovy Map containing sample information
e.g. [ id:'test']
pdbs{:bash}
:file
Input protein structures in PDB format. Files may be gzipped or uncompressed. They should contain exactly one chain!
*.{pdb}
compress{:bash}
: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{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test']
${prefix}.aln${compress ? '.gz' : ''}{:bash}
:file
Alignment in FASTA format. May be gzipped or uncompressed.
*.aln{.gz,}
structure{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test']
${prefix}.pdb${compress ? '.gz' : ''}{:bash}
:file
Overlaid structures in PDB format. May be gzipped or uncompressed.
${prefix}.pdb{.gz,}
versions_mtmalign{:bash}
${task.process}{:bash}
:string
The name of the process
mtm-align{:bash}
:string
The name of the tool
mtm-align -h | sed -n "s/.*Version \([0-9]*\).*/\1/p"{: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
mtm-align{:bash}
:string
The name of the tool
mtm-align -h | sed -n "s/.*Version \([0-9]*\).*/\1/p"{: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
mTM-align
None
Algorithm for structural multiple sequence alignments
