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Bio::Tools::Run::WrappUsersContributed Perl DocBio::Tools::Run::WrapperBase(3)

NAME
       Bio::Tools::Run::WrapperBase - A	Base object for	wrappers around
       executables

SYNOPSIS
	 # do not use this object directly, it provides	the following methods
	 # for its subclasses

	 my $errstr = $obj->error_string();
	 my $exe    = $obj->executable();
	 $obj->save_tempfiles($booleanflag)
	 my $outfile= $obj->outfile_name();
	 my $tempdir= $obj->tempdir(); # get a temporary dir for executing
	 my $io	    = $obj->io;	 # Bio::Root::IO object
	 my $cleanup= $obj->cleanup(); # remove	tempfiles

	 $obj->run({-arg1 => $value});

DESCRIPTION
       This is a basic module from which to build executable wrapper modules.
       It has some basic methods to help when implementing new modules.

FEEDBACK
   Mailing Lists
       User feedback is	an integral part of the	evolution of this and other
       Bioperl modules.	Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About	the mailing lists

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the	problem	with code and
       data examples if	at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of
       the bugs	and their resolution. Bug reports can be submitted via the
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich
       Email jason-at-bioperl.org

CONTRIBUTORS
       Sendu Bala, bix@sendu.me.uk

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   run
	Title	: run
	Usage	: $wrapper->run({ARGS HERE});
	Function: Support generic running with args passed in
		  as a hashref
	Returns	: Depends on the implementation, status	OR data
	Args	: hashref of named arguments

   error_string
	Title	: error_string
	Usage	: $obj->error_string($newval)
	Function: Where	the output from	the last analysis run is stored.
	Returns	: value	of error_string
	Args	: newvalue (optional)

   arguments
	Title	: arguments
	Usage	: $obj->arguments($newval)
	Function: Commandline parameters
	Returns	: value	of arguments
	Args	: newvalue (optional)

   no_param_checks
	Title	: no_param_checks
	Usage	: $obj->no_param_checks($newval)
	Function: Boolean flag as to whether or	not we should
		  trust	the sanity checks for parameter	values
	Returns	: value	of no_param_checks
	Args	: newvalue (optional)

   save_tempfiles
	Title	: save_tempfiles
	Usage	: $obj->save_tempfiles($newval)
	Function: Get/set the choice of	if tempfiles in	the temp dir (see tempdir())
		  are kept or cleaned up. Default is '0', ie. delete temp files.
		  NB: This must	be set to the desired value PRIOR to first creating
		  a temp dir with tempdir(). Any attempt to set	this after tempdir creation will get a warning.
	Returns	: boolean
	Args	: none to get, boolean to set

   outfile_name
	Title	: outfile_name
	Usage	: my $outfile =	$wrapper->outfile_name();
	Function: Get/Set the name of the output file for this run
		  (if you wanted to do something special)
	Returns	: string
	Args	: [optional] string to set value to

   tempdir
	Title	: tempdir
	Usage	: my $tmpdir = $self->tempdir();
	Function: Retrieve a temporary directory name (which is	created)
	Returns	: string which is the name of the temporary directory
	Args	: none

   cleanup
	Title	: cleanup
	Usage	: $wrapper->cleanup();
	Function: Will cleanup the tempdir directory
	Returns	: none
	Args	: none

   io
	Title	: io
	Usage	: $obj->io($newval)
	Function: Gets a Bio::Root::IO object
	Returns	: Bio::Root::IO	object
	Args	: none

   version
	Title	: version
	Usage	: $version = $wrapper->version()
	Function: Returns the program version (if available)
	Returns	: string representing version of the program
	Args	: [Optional] value to (re)set version string

   executable
	Title	: executable
	Usage	: my $exe = $factory->executable();
	Function: Finds	the full path to the executable
	Returns	: string representing the full path to the exe
	Args	: [optional] name of executable	to set path to
		  [optional] boolean flag whether or not warn when exe is not found

   program_path
	Title	: program_path
	Usage	: my $path = $factory->program_path();
	Function: Builds path for executable
	Returns	: string representing the full path to the exe
	Args	: none

   program_dir
	Title	: program_dir
	Usage	: my $dir = $factory->program_dir();
	Function: Abstract get method for dir of program. To be	implemented
		  by wrapper.
	Returns	: string representing program directory
	Args	: none

   program_name
	Title	: program_name
	Usage	: my $name = $factory->program_name();
	Function: Abstract get method for name of program. To be implemented
		  by wrapper.
	Returns	: string representing program name
	Args	: none

   quiet
	Title	: quiet
	Usage	: $factory->quiet(1);
		  if ($factory->quiet()) { ... }
	Function: Get/set the quiet state. Can be used by wrappers to control if
		  program output is printed to the console or not.
	Returns	: boolean
	Args	: none to get, boolean to set

   _setparams()
	Title	: _setparams
	Usage	: $params = $self->_setparams(-params => [qw(window evalue_cutoff)])
	Function: For internal use by wrapper modules to build parameter strings
		  suitable for sending to the program being wrapped. For each method
		  name supplied, calls the method and adds the method name (as modified
		  by optional things) along with its value (unless a switch) to	the
		  parameter string
	Example	: $params = $self->_setparams(-params => [qw(window evalue_cutoff)],
					      -switches	=> [qw(simple large all)],
					      -double_dash => 1,
					      -underscore_to_dash => 1);
		  If window() and simple() had not been	previously called, but
		  evalue_cutoff(0.5), large(1) and all(0) had been called, $params
		  would	be ' --evalue-cutoff 0.5 --large'
	Returns	: parameter string
	Args	: -params => []	or {}  # array ref of method names to call,
					 or hash ref where keys	are method names and
					 values	are how	those names should be output
					 in the	params string
		  -switches => [] or {}# as for	-params, but no	value is printed for
					 these methods
		  -join	=> string      # define	how parameters and their values	are
					 joined, default ' '. (eg. could be '='	for
					 param=value)
		  -lc => boolean       # lc() method names prior to output in string
		  -dash	=> boolean     # prefix	all method names with a	single dash
		  -double_dash => bool # prefix	all method names with a	double dash
		  -mixed_dash => bool  # prefix	single-character method	names with a
				       # single	dash, and multi-character method names
				       # with a	double-dash
		  -underscore_to_dash => boolean # convert all underscores in method
						   names to dashes

perl v5.24.1			  2017-07-08   Bio::Tools::Run::WrapperBase(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | CONTRIBUTORS | APPENDIX

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