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EMBOSS: wossname |
The program has been written on the assumption that most people will use it to quickly find the name of a program based on that program's description, so the output goes to the screen by default.
This program may find some use in automatically generating lists of EMBOSS programs and their groups for Web pages.
Search for programs with 'restrict' in their description % wossname restrict Display a listing of programs in their groups % wossname -search '' Display an alphabetic listing of all programs % wossname -search '' -alphabetic Display only the groups that the programs can belong to % wossname -search '' -groups Output html tags around the list of program groups % wossname '' -groups -html -prelink '#' Output html tags around the list of programs % wossname '' -html -prelink 'http://www.sanger.ac.uk/Software/EMBOSS/Apps/' -postlink '.shtml'
Mandatory qualifiers: [-search] string Enter a word or words here and a case-independent search for it will be made in the one-line documentation of all of the EMBOSS programs. If no keyword is specified, all programs will be listed. Optional qualifiers (* if not always prompted): -outfile outfile If you enter the name of a file here then this program will write the program names and brief descriptions into that file. -html bool If you are sending the output to a file, this will format it for displaying as a table in a WWW document. * -prelink string If you are outputting to a file in HTML format, you can make the program names into hyper-links by setting this to be the first half of the URL. For example, if you wish the program name to be a hyperlink to the URL: http://www.uk.embnet.org/Software/EMBOSS/Apps/programname.html then if you enter http://www.uk.embnet.org/Software/EMBOSS/Apps/ here, then the first half of the URL before the programname will be set. * -postlink string If you are outputting to a file in HTML format, you can make the program names into hyper-links by setting this to be the second half of the URL. For example, if you wish the program name to be a hyperlink to the URL: http://www.uk.embnet.org/Software/EMBOSS/Apps/programname.html then if you enter '.html' here, the second half of the URL after the programname will be set. -groups bool If you use this option, then only the group names will output to the file -alphabetic bool 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. -explode bool 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'. Advanced qualifiers: -[no]emboss bool 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 sheme, ie. they may wish to charge money for them. -[no]embassy bool 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 sheme, ie. they may wish to charge money for them. -colon bool 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. -gui bool 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 General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-search] (Parameter 1) |
Enter a word or words here and a case-independent search for it will be made in the one-line documentation of all of the EMBOSS programs. If no keyword is specified, all programs will be listed. | Any string is accepted | An empty string is accepted |
Optional qualifiers | Allowed values | Default | |
-outfile | If you enter the name of a file here then this program will write the program names and brief descriptions into that file. | Output file | stdout |
-html | If you are sending the output to a file, this will format it for displaying as a table in a WWW document. | Yes/No | No |
-prelink | If you are outputting to a file in HTML format, you can make the program names into hyper-links by setting this to be the first half of the URL. For example, if you wish the program name to be a hyperlink to the URL: http://www.uk.embnet.org/Software/EMBOSS/Apps/programname.html then if you enter http://www.uk.embnet.org/Software/EMBOSS/Apps/ here, then the first half of the URL before the programname will be set. | Any string is accepted | An empty string is accepted |
-postlink | If you are outputting to a file in HTML format, you can make the program names into hyper-links by setting this to be the second half of the URL. For example, if you wish the program name to be a hyperlink to the URL: http://www.uk.embnet.org/Software/EMBOSS/Apps/programname.html then if you enter '.html' here, the second half of the URL after the programname will be set. | Any string is accepted | An empty string is accepted |
-groups | If you use this option, then only the group names will output to the file | Yes/No | No |
-alphabetic | 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. | Yes/No | No |
-explode | 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'. | Yes/No | No |
Advanced qualifiers | Allowed values | Default | |
-[no]emboss | 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 sheme, ie. they may wish to charge money for them. | Yes/No | Yes |
-[no]embassy | 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 sheme, ie. they may wish to charge money for them. | Yes/No | Yes |
-colon | 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. | Yes/No | No |
-gui | 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 | Yes/No | No |
The format of ACD files is documented elsewhere.
------------------------------------------------------------------------------ % wossname 'rest' SEARCH FOR 'REST' redata Isoschizomers, references and suppliers for restriction enzymes restrict Finds restriction enzyme cleavage sites ------------------------------------------------------------------------------
If the -html, -prelink and -postlink qualifiers are specified, then the output will be wrapped in HTML tags, ready for inclusion in a Web page. Note that tags such as <HTML>, <BODY>, </BODY> and </HTML> are not output by this program as the list of programs is expected to form only part of the contents of a web page - the rest of the web page must be supplied by the user.
A program can belong to more than one group.
The name of this program comes from its use as a favorite word of the author Terry Pratchett. It is used especially by the characters of the parrot in Eric and the dog Gaspode in Moving Pictures and Men at Arms.
Program name | Description |
---|---|
infoalign | Information on a multiple sequence alignment |
infoseq | Displays some simple information about sequences |
seealso | Finds programs sharing group names |
showdb | Displays information on the currently available databases |
textsearch | Search sequence documentation text. SRS and Entrez are faster! |
tfm | Displays a program's help documentation manual |