@ISA
=
qw(Bio::Tools::Run::PiseApplication)
;
sub
new {
my
(
$class
,
$location
,
$email
,
@params
) =
@_
;
my
$self
=
$class
->SUPER::new(
$location
,
$email
);
$self
->{COMMAND} =
"einverted"
;
$self
->{VERSION} =
"5.a"
;
$self
->{TITLE} =
"EINVERTED"
;
$self
->{DESCRIPTION} =
"Finds DNA inverted repeats (EMBOSS)"
;
$self
->{OPT_EMAIL} = 0;
$self
->{CATEGORIES} = [
"nucleic:repeats"
,
"nucleic:2d structure"
,
];
$self
->{_INTERFACE_STANDOUT} =
undef
;
$self
->{_STANDOUT_FILE} =
undef
;
$self
->{TOP_PARAMETERS} = [
"einverted"
,
"init"
,
"input"
,
"required"
,
"advanced"
,
"output"
,
"auto"
,
];
$self
->{PARAMETERS_ORDER} = [
"einverted"
,
"init"
,
"input"
,
"sequence"
,
"required"
,
"gap"
,
"threshold"
,
"match"
,
"mismatch"
,
"advanced"
,
"maxrepeat"
,
"output"
,
"outfile"
,
"auto"
,
];
$self
->{TYPE} = {
"einverted"
=>
'String'
,
"init"
=>
'String'
,
"input"
=>
'Paragraph'
,
"sequence"
=>
'Sequence'
,
"required"
=>
'Paragraph'
,
"gap"
=>
'Integer'
,
"threshold"
=>
'Integer'
,
"match"
=>
'Integer'
,
"mismatch"
=>
'Integer'
,
"advanced"
=>
'Paragraph'
,
"maxrepeat"
=>
'Integer'
,
"output"
=>
'Paragraph'
,
"outfile"
=>
'OutFile'
,
"auto"
=>
'String'
,
};
$self
->{FORMAT} = {
"init"
=> {
"perl"
=>
' "" '
,
},
"input"
=> {
},
"sequence"
=> {
"perl"
=>
'" -sequence=$value -sformat=fasta"'
,
},
"required"
=> {
},
"gap"
=> {
"perl"
=>
'" -gap=$value"'
,
},
"threshold"
=> {
"perl"
=>
'" -threshold=$value"'
,
},
"match"
=> {
"perl"
=>
'" -match=$value"'
,
},
"mismatch"
=> {
"perl"
=>
'" -mismatch=$value"'
,
},
"advanced"
=> {
},
"maxrepeat"
=> {
"perl"
=>
'(defined $value && $value != $vdef)? " -maxrepeat=$value" : ""'
,
},
"output"
=> {
},
"outfile"
=> {
"perl"
=>
'" -outfile=$value"'
,
},
"auto"
=> {
"perl"
=>
'" -auto -stdout"'
,
},
"einverted"
=> {
"perl"
=>
'"einverted"'
,
}
};
$self
->{FILENAMES} = {
};
$self
->{SEQFMT} = {
"sequence"
=> [8],
};
$self
->{GROUP} = {
"init"
=> -10,
"sequence"
=> 1,
"gap"
=> 2,
"threshold"
=> 3,
"match"
=> 4,
"mismatch"
=> 5,
"maxrepeat"
=> 6,
"outfile"
=> 7,
"auto"
=> 8,
"einverted"
=> 0
};
$self
->{BY_GROUP_PARAMETERS} = [
"init"
,
"input"
,
"advanced"
,
"required"
,
"output"
,
"einverted"
,
"sequence"
,
"gap"
,
"threshold"
,
"match"
,
"mismatch"
,
"maxrepeat"
,
"outfile"
,
"auto"
,
];
$self
->{SIZE} = {
};
$self
->{ISHIDDEN} = {
"init"
=> 1,
"input"
=> 0,
"sequence"
=> 0,
"required"
=> 0,
"gap"
=> 0,
"threshold"
=> 0,
"match"
=> 0,
"mismatch"
=> 0,
"advanced"
=> 0,
"maxrepeat"
=> 0,
"output"
=> 0,
"outfile"
=> 0,
"auto"
=> 1,
"einverted"
=> 1
};
$self
->{ISCOMMAND} = {
"init"
=> 0,
"input"
=> 0,
"sequence"
=> 0,
"required"
=> 0,
"gap"
=> 0,
"threshold"
=> 0,
"match"
=> 0,
"mismatch"
=> 0,
"advanced"
=> 0,
"maxrepeat"
=> 0,
"output"
=> 0,
"outfile"
=> 0,
"auto"
=> 0,
};
$self
->{ISMANDATORY} = {
"init"
=> 0,
"input"
=> 0,
"sequence"
=> 1,
"required"
=> 0,
"gap"
=> 1,
"threshold"
=> 1,
"match"
=> 1,
"mismatch"
=> 1,
"advanced"
=> 0,
"maxrepeat"
=> 0,
"output"
=> 0,
"outfile"
=> 1,
"auto"
=> 0,
};
$self
->{PROMPT} = {
"init"
=>
""
,
"input"
=>
"input Section"
,
"sequence"
=>
"sequence -- dna [single sequence] (-sequence)"
,
"required"
=>
"required Section"
,
"gap"
=>
"Gap penalty (-gap)"
,
"threshold"
=>
"Minimum score threshold (-threshold)"
,
"match"
=>
"Match score (-match)"
,
"mismatch"
=>
"Mismatch score (-mismatch)"
,
"advanced"
=>
"advanced Section"
,
"maxrepeat"
=>
"Maximum extent of repeats (-maxrepeat)"
,
"output"
=>
"output Section"
,
"outfile"
=>
"outfile (-outfile)"
,
"auto"
=>
""
,
};
$self
->{ISSTANDOUT} = {
"init"
=> 0,
"input"
=> 0,
"sequence"
=> 0,
"required"
=> 0,
"gap"
=> 0,
"threshold"
=> 0,
"match"
=> 0,
"mismatch"
=> 0,
"advanced"
=> 0,
"maxrepeat"
=> 0,
"output"
=> 0,
"outfile"
=> 0,
"auto"
=> 0,
};
$self
->{VLIST} = {
"input"
=> [
'sequence'
,],
"required"
=> [
'gap'
,
'threshold'
,
'match'
,
'mismatch'
,],
"advanced"
=> [
'maxrepeat'
,],
"output"
=> [
'outfile'
,],
};
$self
->{FLIST} = {
};
$self
->{SEPARATOR} = {
};
$self
->{VDEF} = {
"gap"
=>
'12'
,
"threshold"
=>
'50'
,
"match"
=>
'3'
,
"mismatch"
=>
'-4'
,
"maxrepeat"
=>
'4000'
,
"outfile"
=>
'outfile.out'
,
};
$self
->{PRECOND} = {
"init"
=> {
"perl"
=>
'1'
},
"input"
=> {
"perl"
=>
'1'
},
"sequence"
=> {
"perl"
=>
'1'
},
"required"
=> {
"perl"
=>
'1'
},
"gap"
=> {
"perl"
=>
'1'
},
"threshold"
=> {
"perl"
=>
'1'
},
"match"
=> {
"perl"
=>
'1'
},
"mismatch"
=> {
"perl"
=>
'1'
},
"advanced"
=> {
"perl"
=>
'1'
},
"maxrepeat"
=> {
"perl"
=>
'1'
},
"output"
=> {
"perl"
=>
'1'
},
"outfile"
=> {
"perl"
=>
'1'
},
"auto"
=> {
"perl"
=>
'1'
},
};
$self
->{CTRL} = {
};
$self
->{PIPEOUT} = {
};
$self
->{WITHPIPEOUT} = {
};
$self
->{PIPEIN} = {
"sequence"
=> {
"seqfile"
=>
'1'
,
},
};
$self
->{WITHPIPEIN} = {
};
$self
->{ISCLEAN} = {
"init"
=> 0,
"input"
=> 0,
"sequence"
=> 0,
"required"
=> 0,
"gap"
=> 0,
"threshold"
=> 0,
"match"
=> 0,
"mismatch"
=> 0,
"advanced"
=> 0,
"maxrepeat"
=> 0,
"output"
=> 0,
"outfile"
=> 0,
"auto"
=> 0,
};
$self
->{ISSIMPLE} = {
"init"
=> 0,
"input"
=> 0,
"sequence"
=> 1,
"required"
=> 0,
"gap"
=> 1,
"threshold"
=> 1,
"match"
=> 1,
"mismatch"
=> 1,
"advanced"
=> 0,
"maxrepeat"
=> 0,
"output"
=> 0,
"outfile"
=> 1,
"auto"
=> 0,
};
$self
->{PARAMFILE} = {
};
$self
->{COMMENT} = {
"maxrepeat"
=> [
"Maximum separation between the start of repeat and the end of the inverted repeat (the default is 4000 bases)."
,
],
};
$self
->{SCALEMIN} = {
};
$self
->{SCALEMAX} = {
};
$self
->{SCALEINC} = {
};
$self
->{INFO} = {
};
$self
->_init_params(
@params
);
return
$self
;
}
1;