
                              EMBOSS: wossname
     _________________________________________________________________
   
                               Program wossname
                                       
Function

   Finds programs by keywords in their one-line documentation
   
Description

   This allows a user to search for keywords or parts of words in the
   brief documentation (as displayed by a program when it first starts).
   The program name and the brief description is output. If no words to
   search for are specified, then details of all the EMBOSS programs are
   output.
   
   The program has been written on the assumption that most people will
   use it to quickly find the name of a program based on that program's
   description, so the output goes to the screen by default.
   
   This program may find some use in automatically generating lists of
   EMBOSS programs and their groups for Web pages.
   
Usage

   Here are some sample sessions with wossname.

        Search for programs with 'restrict' in their description
        % wossname restrict

        Display a listing of programs in their groups
        % wossname -search ''

        Display an alphabetic listing of all programs
        % wossname -search '' -alphabetic

        Display only the groups that the programs can belong to
        % wossname -search '' -groups
        
        Output html tags around the list of program groups
        % wossname '' -groups -html -prelink '#'

        Output html tags around the list of programs
        % wossname '' -html -prelink
          'http://www.sanger.ac.uk/Software/EMBOSS/Apps/' -postlink '.shtml'

Command line arguments

   Mandatory qualifiers:
  [-search]            string     Enter a word or words here and a
                                  case-independent search for it will be made
                                  in the one-line documentation of all of the
                                  EMBOSS programs. If no keyword is specified,
                                  all programs will be listed.

   Optional qualifiers (* if not always prompted):
   -explode            bool       The groups that EMBOSS applications belong
                                  to have two forms, exploded and not
                                  exploded. The exploded group names are more
                                  numerous and often vaguely phrased than the
                                  non-exploded ones. The exploded names are
                                  formed from definitions of the group names
                                  that start like NAME1:NAME2 and which are
                                  then expanded into many combinations of the
                                  names as: 'NAME1', 'NAME2', 'NAME1 NAME2',
                                  NAME2 NAME1'. The non-expanded names are
                                  simply like: 'NAME1 NAME2'.
   -outfile            outfile    If you enter the name of a file here then
                                  this program will write the program names
                                  and brief descriptions into that file.
   -html               bool       If you are sending the output to a file,
                                  this will format it for displaying as a
                                  table in a WWW document.
*  -prelink            string     If you are outputting to a file in HTML
                                  format, you can make the program names into
                                  hyper-links by setting this to be the first
                                  half of the URL.
                                  For example, if you wish the program name to
                                  be a hyperlink to the URL:
                                  http://www.uk.embnet.org/Software/EMBOSS/Apps
/programname.html
                                  then if you enter
                                  http://www.uk.embnet.org/Software/EMBOSS/Apps
/
                                  here, then the first half of the URL before
                                  the programname will be set.
*  -postlink           string     If you are outputting to a file in HTML
                                  format, you can make the program names into
                                  hyper-links by setting this to be the second
                                  half of the URL.
                                  For example, if you wish the program name to
                                  be a hyperlink to the URL:
                                  http://www.uk.embnet.org/Software/EMBOSS/Apps
/programname.html
                                  then if you enter '.html' here, the second
                                  half of the URL after the programname will
                                  be set.
   -groups             bool       If you use this option, then only the group
                                  names will output to the file
   -alphabetic         bool       If you use this option, then you will get a
                                  single list of the program names and
                                  descriptions instead of the programs being
                                  listed in their functional groups.

   Advanced qualifiers:
   -[no]emboss         bool       If you use this option then EMBOSS program
                                  documentation will be searched. If this
                                  option is set to be false, then only the
                                  EMBASSY programs will be searched (if the
                                  -embassy option is true). EMBASSY programs
                                  are not strictly part of EMBOSS, but use the
                                  same code libraries and share the same look
                                  and feel, but are generally developed by
                                  people who wish the programs to be outside
                                  of the GNU Public Licence sheme, ie. they
                                  may wish to charge money for them.
   -[no]embassy        bool       If you use this option then EMBASSY program
                                  documentation will be searched. If this
                                  option is set to be false, then only the
                                  EMBOSS programs will be searched (if the
                                  -emboss option is true). EMBASSY programs
                                  are not strictly part of EMBOSS, but use the
                                  same code libraries and share the same look
                                  and feel, but are generally developed by
                                  people who wish the programs to be outside
                                  of the GNU Public Licence sheme, ie. they
                                  may wish to charge money for them.
   -colon              bool       The groups that EMBOSS applications belong
                                  to up to two levels, for example the primary
                                  group 'ALIGNMENT' has several sub-groups,
                                  or second-level groups, e.g.: CONSENSUS,
                                  DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL,
                                  MULTIPLE. To aid programs that parse the
                                  output of wossname that require the names of
                                  these subgroups, a colon ':' will be placed
                                  between the first and second level of the
                                  group name if this option is true.
   -gui                bool       This option is intended to help those who
                                  are designing Graphical User Interfaces to
                                  the EMBOSS applications. Some EMBOSS
                                  programs are inappropriate for running in a
                                  GUI, these include other menu programs and
                                  interactive editors. This option allows you
                                  to only report those programs that can be
                                  run from a GUI

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-search]
   (Parameter 1) Enter a word or words here and a case-independent search
   for it will be made in the one-line documentation of all of the EMBOSS
   programs. If no keyword is specified, all programs will be listed. Any
   string is accepted An empty string is accepted
   Optional qualifiers Allowed values Default
   -explode The groups that EMBOSS applications belong to have two forms,
   exploded and not exploded. The exploded group names are more numerous
   and often vaguely phrased than the non-exploded ones. The exploded
   names are formed from definitions of the group names that start like
   NAME1:NAME2 and which are then expanded into many combinations of the
   names as: 'NAME1', 'NAME2', 'NAME1 NAME2', NAME2 NAME1'. The
   non-expanded names are simply like: 'NAME1 NAME2'. Yes/No No
   -outfile If you enter the name of a file here then this program will
   write the program names and brief descriptions into that file. Output
   file stdout
   -html If you are sending the output to a file, this will format it for
   displaying as a table in a WWW document. Yes/No No
   -prelink If you are outputting to a file in HTML format, you can make
   the program names into hyper-links by setting this to be the first
   half of the URL. For example, if you wish the program name to be a
   hyperlink to the URL:
   http://www.uk.embnet.org/Software/EMBOSS/Apps/programname.html then if
   you enter http://www.uk.embnet.org/Software/EMBOSS/Apps/ here, then
   the first half of the URL before the programname will be set. Any
   string is accepted An empty string is accepted
   -postlink If you are outputting to a file in HTML format, you can make
   the program names into hyper-links by setting this to be the second
   half of the URL. For example, if you wish the program name to be a
   hyperlink to the URL:
   http://www.uk.embnet.org/Software/EMBOSS/Apps/programname.html then if
   you enter '.html' here, the second half of the URL after the
   programname will be set. Any string is accepted An empty string is
   accepted
   -groups If you use this option, then only the group names will output
   to the file Yes/No No
   -alphabetic If you use this option, then you will get a single list of
   the program names and descriptions instead of the programs being
   listed in their functional groups. Yes/No No
   Advanced qualifiers Allowed values Default
   -[no]emboss If you use this option then EMBOSS program documentation
   will be searched. If this option is set to be false, then only the
   EMBASSY programs will be searched (if the -embassy option is true).
   EMBASSY programs are not strictly part of EMBOSS, but use the same
   code libraries and share the same look and feel, but are generally
   developed by people who wish the programs to be outside of the GNU
   Public Licence sheme, ie. they may wish to charge money for them.
   Yes/No Yes
   -[no]embassy If you use this option then EMBASSY program documentation
   will be searched. If this option is set to be false, then only the
   EMBOSS programs will be searched (if the -emboss option is true).
   EMBASSY programs are not strictly part of EMBOSS, but use the same
   code libraries and share the same look and feel, but are generally
   developed by people who wish the programs to be outside of the GNU
   Public Licence sheme, ie. they may wish to charge money for them.
   Yes/No Yes
   -colon The groups that EMBOSS applications belong to up to two levels,
   for example the primary group 'ALIGNMENT' has several sub-groups, or
   second-level groups, e.g.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL,
   LOCAL, MULTIPLE. To aid programs that parse the output of wossname
   that require the names of these subgroups, a colon ':' will be placed
   between the first and second level of the group name if this option is
   true. Yes/No No
   -gui This option is intended to help those who are designing Graphical
   User Interfaces to the EMBOSS applications. Some EMBOSS programs are
   inappropriate for running in a GUI, these include other menu programs
   and interactive editors. This option allows you to only report those
   programs that can be run from a GUI Yes/No No
   
Input file format

   The program reads the brief descriptions and the program groups from
   the ACD files. (ACD files control the parameters that the programs
   expect - don't worry about them unless you are writing EMBOSS
   programs).
   
   The format of ACD files is documented elsewhere.
   
Output file format

   The results are written out as a simple list preceded by the group
   that the programs belong to or the word that is being searched for.
   e.g.
------------------------------------------------------------------------------
% wossname 'rest'
SEARCH FOR 'REST'
redata           Isoschizomers, references and suppliers for restriction enzyme
s
restrict         Finds restriction enzyme cleavage sites
------------------------------------------------------------------------------

   If the -html, -prelink and -postlink qualifiers are specified, then
   the output will be wrapped in HTML tags, ready for inclusion in a Web
   page. Note that tags such as <HTML>, <BODY>, </BODY> and </HTML> are
   not output by this program as the list of programs is expected to form
   only part of the contents of a web page - the rest of the web page
   must be supplied by the user.
   
Data files

   As noted above, the program ACD files are searched. The average user
   will not need to worry about this.
   
Notes

   If a program's ACD file does not assign the program to a group, it
   will be automatically assigned to the group 'ASSORTED'.
   
   A program can belong to more than one group.
   
   The name of this program comes from its use as a favorite word of the
   author Terry Pratchett. It is used especially by the characters of the
   parrot in Eric and the dog Gaspode in Moving Pictures and Men at Arms.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0
   
Known bugs

   None.
   
See also

   Program name Description
   infoalign Information on a multiple sequence alignment
   infoseq Displays some simple information about sequences
   seealso Finds programs sharing group names
   showdb Displays information on the currently available databases
   textsearch Search sequence documentation text. SRS and Entrez are
   faster!
   tfm Displays a program's help documentation manual
   whichdb Search all databases for an entry
   
Author(s)

   This application was written by Gary Williams
   (gwilliam@hgmp.mrc.ac.uk)
   
History

   Finished
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
