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abiview.yaml
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abiview.yaml
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!mobyle/program
name: abiview
title: abiview
description: Display the trace in an ABI sequencer file
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
prompt: Input section
name: input
children:
- !mobyle/inputprogramparameter {prompt: Abi sequencing trace file, format: '("",
" -infile=" + str(value))[value is not None]', simple: true, argpos: 1,
mandatory: true, name: infile, command: false}
- !mobyle/inputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/inputprogramparameter {prompt: Name of the output sequence file
(outseq), format: '("" , " -outseq=" + str(value))[value is not None]',
argpos: 2, name: outseq, command: false}
- !mobyle/inputprogramparameter {prompt: Choose the sequence output format,
format: '("", " -osformat=" + str(value))[value is not None and value!=vdef]',
argpos: 3, name: osformat_outseq, command: false}
- !mobyle/inputprogramparameter
prompt: Choose the graph output format
format: (" -graph=" + str(vdef), " -graph=" + str(value))[value is not
None and value!=vdef]
simple: true
argpos: 4
mandatory: true
name: graph
command: false
type: !mobyle/stringtype
default: png
options:
- {label: Png, value: png}
- {label: Gif, value: gif}
- {label: Cps, value: cps}
- {label: Ps, value: ps}
- {label: Meta, value: meta}
- {label: Data, value: data}
- !mobyle/inputprogramparameter
prompt: Name of the output graph
format: ("" , " -goutfile=" + str(value))[value is not None]
argpos: 5
name: xy_goutfile
command: false
type: !mobyle/stringtype {default: abiview_xygraph}
- !mobyle/inputprogramparameter
prompt: First base to report or display (value greater than or equal to
0)
format: ("", " -startbase=" + str(value))[value is not None and value!=vdef]
argpos: 6
name: startbase
command: false
type: !mobyle/integertype {default: 0}
ctrls:
- message: Value greater than or equal to 0 is required
test:
value: {'#gte': '0'}
- !mobyle/inputprogramparameter
comment: Last sequence base to report or display. If the default is set
to zero then the value of this is taken as the maximum number of
bases.
prompt: Last base to report or display
format: ("", " -endbase=" + str(value))[value is not None and value!=vdef]
argpos: 7
name: endbase
command: false
type: !mobyle/integertype {default: 0}
- !mobyle/inputprogramparameter
prompt: Separate the trace graphs for the 4 bases
format: ("", " -separate")[ bool(value) ]
argpos: 8
name: separate
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Display y-axis ticks
format: ("", " -yticks")[ bool(value) ]
argpos: 9
name: yticks
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Display the sequence on the graph
format: (" -nosequence", "")[ bool(value) ]
argpos: 10
name: sequence
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Sequence display window size
format: ("", " -window=" + str(value))[value is not None and value!=vdef]
argpos: 11
name: window
command: false
type: !mobyle/integertype {default: 40}
- !mobyle/inputprogramparameter
prompt: Base graphs to be displayed
format: ("", " -bases=" + str(value))[value is not None and value!=vdef]
argpos: 12
name: bases
command: false
type: !mobyle/stringtype {default: GATC}
- !mobyle/inputprogramparameter
prompt: Turn off any prompting
format: '" -auto -stdout"'
argpos: 12
name: auto
command: false
hidden: true
type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/outputprogramparameter
prompt: Outseq_out option
filenames: outseq
name: outseq_out
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2977']
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.png"'
name: xy_outgraph_png
precond: {graph: png}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.gif"'
name: xy_outgraph_gif
precond: {graph: gif}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.ps"'
name: xy_outgraph_ps
precond:
'#or':
- {graph: ps}
- {graph: cps}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.meta"'
name: xy_outgraph_meta
precond: {graph: meta}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.dat"'
name: xy_outgraph_data
precond: {graph: data}
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"abiview.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"abiview.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0337', 'EDAM_operation:0564']
topics: ['EDAM_topic:0102']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/abiview.html', 'http://emboss.sourceforge.net/docs/themes']
command: abiview
env: {}