/usr/share/EMBOSS/acd/domainalign.acd is in embassy-domalign 0.1.660-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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documentation: "Generate alignments (DAF file) for nodes in
a DCF file."
groups: "Protein:Domains, Alignment:Local"
gui: "yes"
batch: "yes"
cpu: "medium"
embassy: "domalign"
external: "stamp STAMP package http://www.compbio.dundee.ac.uk/"
external: "sorttrans STAMP package http://www.compbio.dundee.ac.uk/"
external: "transform STAMP package http://www.compbio.dundee.ac.uk/"
external: "poststamp STAMP package http://www.compbio.dundee.ac.uk/"
external: "ver2hor STAMP package http://www.compbio.dundee.ac.uk/"
relations: "EDAM_topic:0182 Sequence alignment"
relations: "EDAM_topic:0736 Protein domains and folds"
relations: "EDAM_operation:0292 Sequence alignment construction"
]
section: input [
information: "Input section"
type: "page"
]
infile: dcfinfile [
parameter: "Y"
information: "Domain classification file"
help: "This option specifies the name of DCF file (domain
classification file) (input). A 'domain classification file'
contains classification and other data for domains from SCOP or
CATH, in DCF format (EMBL-like). The files are generated by using
SCOPPARSE and CATHPARSE. Domain sequence information can be added
to the file by using DOMAINSEQS."
knowntype: "Domain classification"
relations: "EDAM_data:0900 Protein domain classification"
]
directory: pdbdir [
parameter: "Y"
information: "Domain pdb directory"
help: "This option specifies the location of domain PDB files
(input). A 'domain PDB file' contains coordinate data for a single
domain from SCOP or CATH, in PDB format. The files are generated
by using DOMAINER."
default: "./"
extension: "ent"
knowntype: "domain pdb"
relations: "EDAM_data:1468 Protein domain"
relations: "EDAM_identifier:1049 Directory name"
]
endsection: input
section: required [
information: "Required section"
type: "page"
]
list: node [
standard: "Y"
default: "1"
minimum: "1"
maximum: "1"
values: "1: Class (SCOP), 2: Fold (SCOP), 3: Superfamily (SCOP),
4: Family (SCOP), 5: Class (CATH), 6: Architecture (CATH), 7:
Topology (CATH), 8: Homologous Superfamily (CATH), 9: Family
(CATH)"
help: "This option specifies the node for redundancy removal.
Redundancy can be removed at any specified node in the SCOP or
CATH hierarchies. For example by selecting 'Class' entries
belonging to the same Class will be non-redundant."
delimiter: ","
codedelimiter: ":"
header: "Node at which to remove redundancy"
information: "Select number."
relations: "EDAM_data:2527 Parameter"
]
list: mode [
standard: "Y"
default: "1"
minimum: "1"
maximum: "1"
values: "1: STAMP, 2: TCOFFEE"
help: "This option specifies the alignment algorithm to use."
delimiter: ","
codedelimiter: ":"
header: "Alignment algorithm option"
information: "Select number."
relations: "EDAM_identifier:1190 Tool name"
]
toggle: keepsinglets [
standard: "Y"
information: "Write sequences of singlet families to file."
help: "This option specifies whether to write sequences of singlet
families to file. If you specify this option, the sequence for
each singlet family are written to file (output)."
default: "Y"
relations: "EDAM_data:2527 Parameter"
]
endsection: required
section: output [
information: "Output section"
type: "page"
]
outdir: dafoutdir [
parameter: "Y"
information: "Domain alignment file output directory"
help: "This option specifies the location of DAF files (domain
alignment files) (output). A 'domain alignment file' contains a
sequence alignment of domains belonging to the same SCOP or CATH
family. The files are in clustal format and are annotated with
domain family classification information. The files generated by
using SCOPALIGN will contain a structure-based sequence alignment
of domains of known structure only. Such alignments can be
extended with sequence relatives (of unknown structure) by using
SEQALIGN."
default: "./"
extension: "daf"
knowntype: "domain alignment"
relations: "EDAM_identifier:1049 Directory name"
relations: "EDAM_data:1384 Sequence alignment (protein)"
]
outdir: singletsoutdir [
standard: "$(keepsinglets)"
information: "Domain hits file output directory"
help: "This option specifies the location of DHF files (domain
hits files) for singlet sequences (output). The singlets are
written out as a 'domain hits file' - which contains database hits
(sequences) with domain classification information, in FASTA
format."
default: "./"
extension: "dhf"
knowntype: "domain hits"
relations: "EDAM_identifier:1049 Directory name"
relations: "EDAM_data:0849 Sequence record"
relations: "EDAM_format:1219 pure protein"
]
outdir: superoutdir [
standard: "@($(mode)==1)"
information: "Pdb entry file output directory"
help: "This option specifies the location of structural
superimposition files (output). A file in PDB format of the
structural superimposition is generated for each family if the
STAMP algorithm is used."
default: "./"
extension: "ent"
knowntype: "pdb"
relations: "EDAM_identifier:1049 Directory name"
relations: "EDAM_data:1481 Structure alignment (protein)"
]
outfile: logfile [
standard: "Y"
information: "Domainatrix log output file"
help: "This option specifies the name of log file (output). The
log file contains messages about any errors arising while
domainalign ran."
default: "domainalign.log"
knowntype: "domainatrix log"
relations: "EDAM_data:1678 Tool log"
]
endsection: output
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