WOSSOPERATION(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

🦋 WOSSOPERATION(1e) — the NAME bit 🦋

okay so bestie, welcome to section 1e of the manual (that's the manual-name part, iykyk), and the star of the show is:

wossoperation — finds programs by EDAM operation ✨

🌸 SYNOPSIS 🌸

like, here's the whole vibe in one go, don't panic, we'll break it down:

wossoperation -identifier string [-explode boolean]
              [-showkeywords boolean] -sensitive boolean
              -subclasses boolean -obsolete boolean -emboss boolean
              -embassy boolean -showembassy string -colon boolean
              -gui boolean [-outfile outfile] [-html toggle]
              [-groups boolean] [-alphabetic boolean]

wossoperation -help

💜 DESCRIPTION 💜

wossoperation is a command line program straight out of EMBOSS — that's “the European Molecular Biology Open Software Suite”, the iconic one 🧬👑.

It's part of the "Ontology:EDAM,Documentation" command group(s). periodt.

✨ OPTIONS ✨

🎀 Input section 🎀

  • -identifier string — yeah, this one takes a string. That's the whole note. slay.

🍓 Additional section 🍓

  • -explode boolean — okay so 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 (not me being shady, that's literally in the docs 💀). 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
  • -showkeywords boolean — Default value: N

💅 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 — extends 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 go 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

🫶 Output section 🫶

  • -outfile outfile — Default value: stdout

🌈 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

😭 BUGS 😭

Found a bug? Not the vibe, but okay, report it. Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). 🐛💀

👀 SEE ALSO 👀

wossoperation is fully documented via the tfm(1) system. so like, go read that too bestie 📚

🎀 AUTHOR 🎀

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • Wrote the script used to autogenerate this manual page. iconic behaviour honestly 🫶

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.

and that's the whole page, no cap 🌸

kisses, this was EMBOSS 6.4.0, dated 05/11/2012 — see u next time, bestie 💅✨

📦 where this page comes from