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combine_??.yaml
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combine_??.yaml
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!mobyle/program
name: combine
version: ??
title: Combine
description: Combine multiple sequence alignments
authors: ??
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparameter
prompt: initiation
format: '" -n 1 -W 12 -o std.out -e std.err -N __bsubArgsEnd__ java -jar /home/mobyle/www/mobyleDev/bin/Combine.jar
"'
argpos: 0
name: bsubinit
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparagraph
prompt: General settings
name: general
children:
- !mobyle/inputprogramparameter
prompt: Enter name of combined sequence file (union of all files)
format: ( "" , str( value))[ value is not None ]
argpos: 1
name: union
command: false
type: !mobyle/stringtype {default: combine_union.phy}
- !mobyle/inputprogramparameter
prompt: Enter name of combined sequence file (intersection of all files)
format: ( "" , " -i " + str( value))[ value is not None ]
argpos: 2
name: intersect
command: false
type: !mobyle/stringtype {default: combine_intersect.phy}
- !mobyle/inputprogramparameter
prompt: Remove taxa(rows) from alignment?
format: ( "" , " -rr " )[ value ]
argpos: 3
name: row
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Range of rows to remove (use commas with no spaces for multiple
entries)
format: ( "" , str( value) + " ")[ row ]
argpos: 4
name: rrange
command: false
type: !mobyle/stringtype {default: x-y}
- !mobyle/inputprogramparameter
prompt: Exclude sites(columns) in alignment?
format: ( "" , " -rc " )[ value ]
argpos: 5
name: column
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Range of columns to remove (use commas with no spaces for multiple
entries)
format: ( "" , str( value) + " ")[ column ]
argpos: 6
name: crange
command: false
type: !mobyle/stringtype {default: x-y}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 11, name: infile1, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 12, name: infile2, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 13, name: infile3, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 14, name: infile4, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 15, name: infile5, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 16, name: infile6, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 17, name: infile7, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 18, name: infile8, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 19, name: infile9, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 20, name: infile10, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 21, name: infile11, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 22, name: infile12, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 23, name: infile13, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 24, name: infile14, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 25, name: infile15, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 26, name: infile16, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 27, name: infile17, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 28, name: infile18, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 29, name: infile19, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 30, name: infile20, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 31, name: infile21, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 32, name: infile22, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 33, name: infile23, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 34, name: infile24, command: false}
- !mobyle/inputprogramparameter {prompt: files to be combined CLUSTAL (.aln)
NEXUS (.nxs) or PHYLIP (.phy), format: '( "" , " " + str( value ))[
value is not None ]', argpos: 35, name: infile25, command: false}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparameter {filenames: '"std.out"', name: stdoutfile}
- !mobyle/outputprogramparagraph
prompt: General settings
name: general
children:
- !mobyle/outputprogramparameter {prompt: Output file, filenames: str(union),
name: unionout}
- !mobyle/outputprogramparameter {prompt: Output file, filenames: str(intersect),
name: intersectout}
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"combine.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"combine.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
references:
- {doi: null, label: '??', url: null}
command: runbsub
env: {}