wossoperation 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 Finds programs by EDAM operation Description wossoperation 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 operation 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 operation annotation. Usage Here is a sample session with wossoperation Search for programs with 'codon' in their operation: % wossoperation codon Finds programs by EDAM operation SEARCH FOR OPERATION 'CODON' cai Calculate codon adaptation index chips Calculates 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) syco Draw synonymous codon usage statistic plot for a nucleotide sequence wobble Plot third base position variability in a nucleotide sequence Command line arguments Finds programs by EDAM operation Version: EMBOSS:6.4.0.0 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 wossoperation 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 Finds programs with similar function to a specified program tfm Displays full documentation for an application wossdata Finds programs by EDAM data wossinput Finds programs by EDAM input data wossname Finds programs by keywords in their short description wossoutput Finds programs by EDAM output data wossparam Finds programs by EDAM parameter wosstopic Finds programs by EDAM topic 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