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dan.yaml
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dan.yaml
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!mobyle/program
name: dan
title: dan
description: Calculates nucleic acid melting temperature
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
prompt: Input section
name: input
children:
- !mobyle/inputprogramparameter
prompt: Sequence option
format: ("", " -sequence=" + str(value))[value is not None]
simple: true
argpos: 1
mandatory: true
name: sequence
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:1927', 'EDAM_format:2200', 'EDAM_format:1935',
'EDAM_format:1936', 'EDAM_format:1948', 'EDAM_format:1948', 'EDAM_format:1957',
'EDAM_format:2188']
data_terms: ['EDAM_data:2977']
- !mobyle/inputprogramparagraph
prompt: Required section
name: required
children:
- !mobyle/inputprogramparameter
comment: The values of melting point and other thermodynamic properties
of the sequence are determined by taking a short length of sequence
known as a window and determining the properties of the sequence
in that window. The window is incrementally moved along the sequence
with the properties being calculated at each new position.
prompt: Enter window size (value from 1 to 100)
format: ("", " -windowsize=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 2
mandatory: true
name: windowsize
command: false
type: !mobyle/integertype {default: 20}
ctrls:
- message: Value greater than or equal to 1 is required
test:
value: {'#gte': '1'}
- message: Value less than or equal to 100 is required
test:
value: {'#lte': '100'}
- !mobyle/inputprogramparameter
comment: This is the amount by which the window is moved at each increment
in order to find the melting point and other properties along the
sequence.
prompt: Enter shift increment (value greater than or equal to 1)
format: ("", " -shiftincrement=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 3
mandatory: true
name: shiftincrement
command: false
type: !mobyle/integertype {default: 1}
ctrls:
- message: Value greater than or equal to 1 is required
test:
value: {'#gte': '1'}
- !mobyle/inputprogramparameter
prompt: Enter dna concentration (nm) (value from 1. to 100000.)
format: ("", " -dnaconc=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 4
mandatory: true
name: dnaconc
command: false
type: !mobyle/floattype {default: 50.0}
ctrls:
- message: Value greater than or equal to 1. is required
test:
value: {'#gte': '1.0'}
- message: Value less than or equal to 100000. is required
test:
value: {'#lte': '100000.0'}
- !mobyle/inputprogramparameter
prompt: Enter salt concentration (mm) (value from 1. to 1000.)
format: ("", " -saltconc=" + str(value))[value is not None and value!=vdef]
simple: true
argpos: 5
mandatory: true
name: saltconc
command: false
type: !mobyle/floattype {default: 50.0}
ctrls:
- message: Value greater than or equal to 1. is required
test:
value: {'#gte': '1.0'}
- message: Value less than or equal to 1000. is required
test:
value: {'#lte': '1000.0'}
- !mobyle/inputprogramparagraph
prompt: Additional section
name: additional
children:
- !mobyle/inputprogramparagraph
prompt: Product options
name: productsection
children:
- !mobyle/inputprogramparameter
comment: This prompts for percent formamide, percent of mismatches
allowed and product length.
prompt: Prompt for product values
format: ("", " -product")[ bool(value) ]
argpos: 6
name: product
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: This specifies the percent formamide to be used in calculations
(it is ignored unless -product is used).
prompt: Enter percentage of formamide (value from 0. to 100.)
format: ("", " -formamide=" + str(value))[value is not None and value!=vdef]
argpos: 7
name: formamide
precond: product
command: false
type: !mobyle/floattype {default: 0.0}
ctrls:
- message: Value greater than or equal to 0. is required
test:
value: {'#gte': '0.0'}
- message: Value less than or equal to 100. is required
test:
value: {'#lte': '100.0'}
- !mobyle/inputprogramparameter
comment: This specifies the percent mismatch to be used in calculations
(it is ignored unless -product is used).
prompt: Enter percent mismatch (value from 0. to 100.)
format: ("", " -mismatch=" + str(value))[value is not None and value!=vdef]
argpos: 8
name: mismatch
precond: product
command: false
type: !mobyle/floattype {default: 0.0}
ctrls:
- message: Value greater than or equal to 0. is required
test:
value: {'#gte': '0.0'}
- message: Value less than or equal to 100. is required
test:
value: {'#lte': '100.0'}
- !mobyle/inputprogramparameter
comment: This specifies the product length to be used in calculations
(it is ignored unless -product is used).
prompt: Enter the product length
format: ("", " -prodlen=" + str(value))[value is not None]
argpos: 9
name: prodlen
precond:
'#and': [product, windowsize]
command: false
type: !mobyle/integertype {}
- !mobyle/inputprogramparagraph
prompt: Thermodynamic options
name: thermosection
children:
- !mobyle/inputprogramparameter
comment: Output the DeltaG, DeltaH and DeltaS values of the sequence
windows to the output data file.
prompt: Thermodynamic calculations
format: ("", " -thermo")[ bool(value) ]
argpos: 10
name: thermo
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: If -thermo has been specified then this specifies the temperature
at which to calculate the DeltaG, DeltaH and DeltaS values.
prompt: Enter temperature (value from 0. to 100.)
format: ("", " -temperature=" + str(value))[value is not None and
value!=vdef]
argpos: 11
name: temperature
precond: thermo
command: false
type: !mobyle/floattype {default: 25.0}
ctrls:
- message: Value greater than or equal to 0. is required
test:
value: {'#gte': '0.0'}
- message: Value less than or equal to 100. is required
test:
value: {'#lte': '100.0'}
- !mobyle/inputprogramparagraph
prompt: Advanced section
name: advanced
children:
- !mobyle/inputprogramparameter
comment: This specifies that the sequence is an RNA sequence and not a
DNA sequence.
prompt: Use rna data values
format: ("", " -rna")[ bool(value) ]
argpos: 12
name: rna
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/inputprogramparameter
comment: If this is not specified then the file of output data is produced,
else a plot of the melting point along the sequence is produced.
prompt: Produce a plot
format: ("", " -plot")[ bool(value) ]
argpos: 13
name: plot
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: Enter a minimum value for the temperature scale (y-axis) of the
plot.
prompt: Enter minimum temperature (value from 0. to 150.)
format: ("", " -mintemp=" + str(value))[value is not None and value!=vdef]
argpos: 14
name: mintemp
precond: plot
command: false
type: !mobyle/floattype {default: 55.0}
ctrls:
- message: Value greater than or equal to 0. is required
test:
value: {'#gte': '0.0'}
- message: Value less than or equal to 150. is required
test:
value: {'#lte': '150.0'}
- !mobyle/inputprogramparameter
prompt: Choose the graph output format
format: (" -graph=" + str(vdef), " -graph=" + str(value))[value is not
None and value!=vdef]
argpos: 15
name: graph
precond: plot
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: 16
name: xy_goutfile
precond: plot
command: false
type: !mobyle/stringtype {default: dan_xygraph}
- !mobyle/inputprogramparameter
comment: If a plot is not being produced then data on the melting point
etc. in each window along the sequence is output to the file.
prompt: Name of the report file
format: ("" , " -outfile=" + str(value))[value is not None]
argpos: 17
name: outfile
precond: {'#not': plot}
command: false
type: !mobyle/stringtype {default: dan.report}
- !mobyle/inputprogramparameter
prompt: Choose the report output format
format: ("", " -rformat=" + str(value))[value is not None and value!=vdef]
argpos: 18
name: rformat_outfile
precond: {'#not': plot}
command: false
type: !mobyle/stringtype
default: SEQTABLE
options:
- {label: Dasgff, value: DASGFF}
- {label: Dbmotif, value: DBMOTIF}
- {label: Diffseq, value: DIFFSEQ}
- {label: Embl, value: EMBL}
- {label: Excel, value: EXCEL}
- {label: Feattable, value: FEATTABLE}
- {label: Genbank, value: GENBANK}
- {label: Gff, value: GFF}
- {label: Listfile, value: LISTFILE}
- {label: Motif, value: MOTIF}
- {label: Nametable, value: NAMETABLE}
- {label: Pir, value: PIR}
- {label: Regions, value: REGIONS}
- {label: Seqtable, value: SEQTABLE}
- {label: Simple, value: SIMPLE}
- {label: Srs, value: SRS}
- {label: Swiss, value: SWISS}
- {label: Table, value: TABLE}
- {label: Tagseq, value: TAGSEQ}
- !mobyle/inputprogramparameter
prompt: Turn off any prompting
format: '" -auto -stdout"'
argpos: 19
name: auto
command: false
hidden: true
type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparagraph
prompt: Output section
name: output
children:
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.png"'
name: xy_outgraph_png
precond:
'#and':
- plot
- {graph: png}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.gif"'
name: xy_outgraph_gif
precond:
'#and':
- plot
- {graph: gif}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.ps"'
name: xy_outgraph_ps
precond:
'#or':
- '#and':
- plot
- {graph: ps}
- {graph: cps}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.meta"'
name: xy_outgraph_meta
precond:
'#and':
- plot
- {graph: meta}
- !mobyle/outputprogramparameter
prompt: Graph file
filenames: '"*.dat"'
name: xy_outgraph_data
precond:
'#and':
- plot
- {graph: data}
- !mobyle/outputprogramparameter
prompt: Outfile_out option
filenames: outfile
name: outfile_out
precond:
rformat_outfile:
'#in': [DASGFF, DBMOTIF, DIFFSEQ, EMBL, EXCEL, FEATTABLE, GENBANK,
GFF, LISTFILE, MOTIF, NAMETABLE, PIR, REGIONS, SEQTABLE, SIMPLE,
SRS, SWISS, TABLE, TAGSEQ]
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"dan.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"dan.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0455']
topics: ['EDAM_topic:0104']
documentation_links: ['http://bioweb2.pasteur.fr/docs/EMBOSS/dan.html', 'http://emboss.sourceforge.net/docs/themes']
command: dan
env: {}