Additional section¶
-explode boolean
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'. Default value: N
-allmatch boolean
By default, all words in the search string must match.
This option searches for a match to any word in a list of possibilities
Default value: Y
-showkeywords boolean
Default value: N
Advanced section¶
-emboss boolean
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 General Public License scheme Default value:
Y
-embassy boolean
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 General Public License scheme Default value:
Y
-showembassy string
If you use this option then this EMBASSY package program
documentation will be searched. 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 General Public License scheme
-colon boolean
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. Note: This does not
apply if the group names have been exploded with the 'explode' option. Default
value: N
-gui boolean
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 Default value: N
Html section¶
-html toggle
If you are sending the output to a file, this will format
it for displaying as a table in a WWW document. Default value: N
-groups boolean
If you use this option, then only the group names will be
output to the file Default value: N
-alphabetic boolean
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. Default value: N
