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closestBed_2.15.0.yaml
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!mobyle/program
name: closestBed
version: 2.15.0
title: 'BEDtools: closestBED'
description: For each feature in A, finds the closest feature (upstream or downstream)
in B
authors: Quinlan A.R. & Hall I.M.
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
prompt: Input
name: input_para
children:
- !mobyle/inputprogramparameter
prompt: Genome Annotation data A (BED/GFF/VCF format) [-a]
format: '" -a " + str( value )'
simple: true
argpos: 1
mandatory: true
name: input_bed_fileA
command: false
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparameter
prompt: Genome Annotation data B (BED/GFF/VCF format) [-b]
format: '" -b " + str( value )'
simple: true
argpos: 2
mandatory: true
name: input_bed_fileB
command: false
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparagraph
prompt: Options
name: options_para
children:
- !mobyle/inputprogramparameter
comment: 'Default option: overlaps are reported without respect to strand.Same
strandedness option: find the closest feature in B that overlaps A
on the _same_ strand.Opposite strandedness option: find the closest
feature in B that overlaps A on the _opposite_ strand.'
prompt: Strandedness (-s or -S)
format: ("", " " + str(value))[value is not None and value!=vdef]
argpos: 3
name: force_strand_option
command: false
type: !mobyle/stringtype
default: ignore
options:
- {label: ignore strandedness (default), value: ignore}
- {label: Same strandedness, value: -s}
- {label: Opposite strandedness, value: -S}
- !mobyle/inputprogramparameter
comment: How ties for closest feature are handled. This occurs when two
features in B have exactly the same overlap with A. By default, all
such features in B are reported.
prompt: Tie handling (-t)
format: ("" + str(vdef), " -t " + str(value))[value is not None and value!=vdef]
argpos: 4
name: tile_handling_option
command: false
type: !mobyle/stringtype
default: all
options:
- {label: Report all ties, value: all}
- {label: Report the first tie that occurred in the B data, value: first}
- {label: Report the last tie that occurred in the B data, value: last}
- !mobyle/inputprogramparameter
comment: In addition to the closest feature in B, report its distance
to A as an extra column.The reported distance for overlapping features
will be 0.
prompt: Report distance to A as extra column (-d)
format: ('',' -d ')[value==1]
argpos: 5
name: output_distance
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: "Like -d, report the closest feature in B, and its distance to\
\ A as an extra column. Unlike -d, use negative distances to report\
\ \t\tupstream features. \t\tThe options for defining which orientation\
\ is \"upstream\" are: \t\t- \"ref\" Report distance with respect\
\ to the reference genome. \t\t B features with a lower\
\ (start, stop) are upstream \t\t- \"a\" Report distance with\
\ respect to A. \t\t When A is on the - strand, \"upstream\"\
\ means B has a \t\t higher (start,stop). \t\t- \"b\" \
\ Report distance with respect to B. \t\t When B is\
\ on the - strand, \"upstream\" means A has a \t\t higher\
\ (start,stop)."
prompt: Report distance with orientation (-D)
format: ('', ' -D ' + str(value))[value is not None and value != vdef]
argpos: 6
name: output_distance_orientation
command: false
type: !mobyle/stringtype
default: default
options:
- {label: Do not report distance with orientation, value: default}
- {label: Report distance with respect to the reference genome., value: ref}
- {label: Report distance with respect to A., value: a}
- {label: Report distance with respect to B., value: b}
- !mobyle/inputprogramparameter
comment: we want close, yet not touching features only.
prompt: Ignore features in B that overlap A (-io)
format: ('',' -io ')[value==1]
argpos: 7
name: output_overlap_feature
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Output
name: Output
children:
- !mobyle/inputprogramparameter
prompt: Output file name
format: (" > " + str(vdef) , " > " + str(value))[value is not None]
simple: true
argpos: 8
mandatory: true
name: outfile
command: false
type: !mobyle/stringtype {default: closest_feature.txt}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"closestBed.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"closestBed.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:3194']
topics: ['EDAM_topic:0160']
command: closestBed
env: {}