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