Advanced section¶
-sensitive boolean
By default, the query keywords are matched against the
EDAM term names (and synonyms) only. This option also matches the keywords
against the EDAM term definitions and will therefore (typically) report more
matches. Default value: N
-subclasses boolean
Extend the query matches to include all terms which are
specialisations (EDAM sub-classes) of the matched type. Default value: Y
-obsolete boolean
The default behaviour is to not use or return obsolete
terms. This option if set will include all terms. Default value: N
-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
