                                  wosstopic



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Find programs by EDAM topic

Description

   wosstopic searches the annotation of applications in ACD files, using
   terms from the EDAM ontology. There are various options for controlling
   how the search is performed and what is given in the output file.
   Optionally, the output will be wrapped in HTML tags ready for inclusion
   in a Web page.

Algorithm

   The first search is of the EDAM ontology topic namespace, using the
   term names and their synonynms. All child terms are automatically
   included in the set of matches inless the -nosubclasses qualifier is
   used.

   The -sensitive qualifier also searches the definition strings.

   The set of EDAM terms are then compared to relations in the ACD file,
   where the application definition requires EDAM topic annotation.

Usage

   Here is a sample session with wosstopic

   Search for programs with 'codon' in their topic:


% wosstopic codon
Find programs by EDAM topic

SEARCH FOR TOPIC 'CODON'
cai         Calculate codon adaptation index
chips       Calculate Nc codon usage statistic
codcmp      Codon usage table comparison
codcopy     Copy and reformat a codon usage table
cusp        Create a codon usage table from nucleotide sequence(s)
cutgextract Extract codon usage tables from CUTG database
syco        Draw synonymous codon usage statistic plot for a nucleotide sequence



Command line arguments

Find programs by EDAM topic
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-identifier]        string     Identifier(s) to search for in ontology (Any
                                  string)

   Additional (Optional) qualifiers:
   -explode            boolean    [N] 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'.
   -showkeywords       boolean    [N] Show keywords with program documentation
   -outfile            outfile    [stdout] Tool metadata output file
   -html               toggle     [N] If you are sending the output to a file,
                                  this will format it for displaying as a
                                  table in a WWW document.
   -groups             boolean    [N] If you use this option, then only the
                                  group names will be output to the file
   -alphabetic         boolean    [N] 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 (Unprompted) qualifiers:
   -sensitive          boolean    [N] 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.
   -[no]subclasses     boolean    [Y] Extend the query matches to include all
                                  terms which are specialisations (EDAM
                                  sub-classes) of the matched type.
   -obsolete           boolean    [N] The default behaviour is to not use or
                                  return obsolete terms. This option if set
                                  will include all terms.
   -[no]emboss         boolean    [Y] 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 scheme
   -[no]embassy        boolean    [Y] 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 scheme
   -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
                                  Public Licence scheme (Any string)
   -colon              boolean    [N] 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.
   -gui                boolean    [N] 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

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


Input file format

   wosstopic 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).

Output file format

   The results are written out as a simple list of program names and short
   descriptions.

Data files

   The EDAM Ontology is included in EMBOSS as local database edam.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

                     Program name                         Description
                    drfinddata     Find public databases by data type
                    drfindformat   Find public databases by format
                    drfindid       Find public databases by identifier
   drfindresource   Find public databases by resource
                    edamdef        Find EDAM ontology terms by definition
                    edamhasinput   Find EDAM ontology terms by has_input relation
                    edamhasoutput  Find EDAM ontology terms by has_output relation
                    edamisformat   Find EDAM ontology terms by is_format_of relation
                    edamisid       Find EDAM ontology terms by is_identifier_of relation
                    edamname       Find EDAM ontology terms by name
                    seealso        Find programs with similar function to a specified program
                    tfm            Display full documentation for an application
                    wossdata       Find programs by EDAM data
                    wossinput      Find programs by EDAM input data
                    wossname       Find programs by keywords in their short description
                    wossoperation  Find programs by EDAM operation
                    wossoutput     Find programs by EDAM output data
                    wossparam      Find programs by EDAM parameter

Author(s)

   Peter            Rice
   European         Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton,         Cambridge CB10 1SD, UK

                    Please report all bugs to the EMBOSS bug team
                    (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

Target users

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

Comments

                    None
