— — |
@ISA = qw(Bio::Tools::Run::PiseApplication) ;
sub new {
my ( $class , $location , $email , @params ) = @_ ;
my $self = $class ->SUPER::new( $location , $email );
$self ->{COMMAND} = "findkm" ;
$self ->{VERSION} = "5.a" ;
$self ->{TITLE} = "FINDKM" ;
$self ->{DESCRIPTION} = "Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot (EMBOSS)" ;
$self ->{OPT_EMAIL} = 0;
$self ->{CATEGORIES} = [
"enzyme kinetics" ,
];
$self ->{_INTERFACE_STANDOUT} = undef ;
$self ->{_STANDOUT_FILE} = undef ;
$self ->{TOP_PARAMETERS} = [
"findkm" ,
"init" ,
"input" ,
"advanced" ,
"output" ,
"auto" ,
"psouput" ,
"psresults" ,
"metaresults" ,
"dataresults" ,
"pngresults" ,
];
$self ->{PARAMETERS_ORDER} = [
"findkm" ,
"init" ,
"input" ,
"infile" ,
"advanced" ,
"plot" ,
"output" ,
"outfile" ,
"graphlb" ,
"auto" ,
"psouput" ,
"psresults" ,
"metaresults" ,
"dataresults" ,
"pngresults" ,
];
$self ->{TYPE} = {
"findkm" => 'String' ,
"init" => 'String' ,
"input" => 'Paragraph' ,
"infile" => 'InFile' ,
"advanced" => 'Paragraph' ,
"plot" => 'Switch' ,
"output" => 'Paragraph' ,
"outfile" => 'OutFile' ,
"graphlb" => 'Excl' ,
"auto" => 'String' ,
"psouput" => 'String' ,
"psresults" => 'Results' ,
"metaresults" => 'Results' ,
"dataresults" => 'Results' ,
"pngresults" => 'Results' ,
};
$self ->{FORMAT} = {
"init" => {
"perl" => ' "" ' ,
},
"input" => {
},
"infile" => {
"perl" => '" -infile=$value"' ,
},
"advanced" => {
},
"plot" => {
"perl" => '($value)? "" : " -noplot"' ,
},
"output" => {
},
"outfile" => {
"perl" => '" -outfile=$value"' ,
},
"graphlb" => {
"perl" => '($value)? " -graphlb=$value" : ""' ,
},
"auto" => {
"perl" => '" -auto -stdout"' ,
},
"psouput" => {
"perl" => '" -goutfile=findkm"' ,
},
"psresults" => {
},
"metaresults" => {
},
"dataresults" => {
},
"pngresults" => {
},
"findkm" => {
"perl" => '"findkm"' ,
}
};
$self ->{FILENAMES} = {
"psresults" => '*.ps' ,
"metaresults" => '*.meta' ,
"dataresults" => '*.dat' ,
"pngresults" => '*.png *.2 *.3' ,
};
$self ->{SEQFMT} = {
};
$self ->{GROUP} = {
"init" => -10,
"infile" => 1,
"plot" => 2,
"outfile" => 3,
"graphlb" => 4,
"auto" => 5,
"psouput" => 100,
"findkm" => 0
};
$self ->{BY_GROUP_PARAMETERS} = [
"init" ,
"input" ,
"findkm" ,
"advanced" ,
"output" ,
"psresults" ,
"metaresults" ,
"dataresults" ,
"pngresults" ,
"infile" ,
"plot" ,
"outfile" ,
"graphlb" ,
"auto" ,
"psouput" ,
];
$self ->{SIZE} = {
};
$self ->{ISHIDDEN} = {
"init" => 1,
"input" => 0,
"infile" => 0,
"advanced" => 0,
"plot" => 0,
"output" => 0,
"outfile" => 0,
"graphlb" => 0,
"auto" => 1,
"psouput" => 1,
"psresults" => 0,
"metaresults" => 0,
"dataresults" => 0,
"pngresults" => 0,
"findkm" => 1
};
$self ->{ISCOMMAND} = {
"init" => 0,
"input" => 0,
"infile" => 0,
"advanced" => 0,
"plot" => 0,
"output" => 0,
"outfile" => 0,
"graphlb" => 0,
"auto" => 0,
"psouput" => 0,
"psresults" => 0,
"metaresults" => 0,
"dataresults" => 0,
"pngresults" => 0,
};
$self ->{ISMANDATORY} = {
"init" => 0,
"input" => 0,
"infile" => 1,
"advanced" => 0,
"plot" => 0,
"output" => 0,
"outfile" => 1,
"graphlb" => 0,
"auto" => 0,
"psouput" => 0,
"psresults" => 0,
"metaresults" => 0,
"dataresults" => 0,
"pngresults" => 0,
};
$self ->{PROMPT} = {
"init" => "" ,
"input" => "input Section" ,
"infile" => "Enter name of file containing data (-infile)" ,
"advanced" => "advanced Section" ,
"plot" => "S/V vs S (-plot)" ,
"output" => "output Section" ,
"outfile" => "outfile (-outfile)" ,
"graphlb" => "graphlb (-graphlb)" ,
"auto" => "" ,
"psouput" => "" ,
"psresults" => "" ,
"metaresults" => "" ,
"dataresults" => "" ,
"pngresults" => "" ,
};
$self ->{ISSTANDOUT} = {
"init" => 0,
"input" => 0,
"infile" => 0,
"advanced" => 0,
"plot" => 0,
"output" => 0,
"outfile" => 0,
"graphlb" => 0,
"auto" => 0,
"psouput" => 0,
"psresults" => 0,
"metaresults" => 0,
"dataresults" => 0,
"pngresults" => 0,
};
$self ->{VLIST} = {
"input" => [ 'infile' ,],
"advanced" => [ 'plot' ,],
"output" => [ 'outfile' , 'graphlb' ,],
"graphlb" => [ 'x11' , 'x11' , 'hp7470' , 'hp7470' , 'postscript' , 'postscript' , 'cps' , 'cps' , 'hp7580' , 'hp7580' , 'null' , 'null' , 'data' , 'data' , 'colourps' , 'colourps' , 'text' , 'text' , 'none' , 'none' , 'tek4107t' , 'tek4107t' , 'tekt' , 'tekt' , 'xwindows' , 'xwindows' , 'hpgl' , 'hpgl' , 'xterm' , 'xterm' , 'meta' , 'meta' , 'ps' , 'ps' , 'tek' , 'tek' , 'png' , 'png' , 'tektronics' , 'tektronics' ,],
};
$self ->{FLIST} = {
};
$self ->{SEPARATOR} = {
};
$self ->{VDEF} = {
"plot" => '1' ,
"outfile" => 'outfile.out' ,
"graphlb" => 'postscript' ,
};
$self ->{PRECOND} = {
"init" => { "perl" => '1' },
"input" => { "perl" => '1' },
"infile" => { "perl" => '1' },
"advanced" => { "perl" => '1' },
"plot" => { "perl" => '1' },
"output" => { "perl" => '1' },
"outfile" => { "perl" => '1' },
"graphlb" => { "perl" => '1' },
"auto" => { "perl" => '1' },
"psouput" => {
"perl" => '$graphlb eq "postscript" || $graphlb eq "ps" || $graphlb eq "colourps" || $graphlb eq "cps" || $graphlb eq "png"' ,
},
"psresults" => {
"perl" => '$graphlb eq "postscript" || $graphlb eq "ps" || $graphlb eq "colourps" || $graphlb eq "cps"' ,
},
"metaresults" => {
"perl" => '$graphlb eq "meta"' ,
},
"dataresults" => {
"perl" => '$graphlb eq "data"' ,
},
"pngresults" => {
"perl" => '$graphlb eq "png"' ,
},
};
$self ->{CTRL} = {
};
$self ->{PIPEOUT} = {
};
$self ->{WITHPIPEOUT} = {
};
$self ->{PIPEIN} = {
};
$self ->{WITHPIPEIN} = {
};
$self ->{ISCLEAN} = {
"init" => 0,
"input" => 0,
"infile" => 0,
"advanced" => 0,
"plot" => 0,
"output" => 0,
"outfile" => 0,
"graphlb" => 0,
"auto" => 0,
"psouput" => 0,
"psresults" => 0,
"metaresults" => 0,
"dataresults" => 0,
"pngresults" => 0,
};
$self ->{ISSIMPLE} = {
"init" => 0,
"input" => 0,
"infile" => 1,
"advanced" => 0,
"plot" => 0,
"output" => 0,
"outfile" => 1,
"graphlb" => 0,
"auto" => 0,
"psouput" => 0,
"psresults" => 0,
"metaresults" => 0,
"dataresults" => 0,
"pngresults" => 0,
};
$self ->{PARAMFILE} = {
};
$self ->{COMMENT} = {
};
$self ->{SCALEMIN} = {
};
$self ->{SCALEMAX} = {
};
$self ->{SCALEINC} = {
};
$self ->{INFO} = {
};
$self ->_init_params( @params );
return $self ;
}
1;
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