1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
|
wossdata
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 data
Description
wossdata searches the annotation of application inputs and outputs 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 data 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 input, output and parameter definitions require data references.
Usage
Here is a sample session with wossdata
Search for programs with 'codon' in their input, output or parameters
% wossdata codon
Find programs by EDAM data
SEARCH FOR DATA 'CODON'
backtranseq Back-translate a protein sequence to a nucleotide sequence
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
makenucseq Create random nucleotide sequences
syco Draw synonymous codon usage statistic plot for a nucleotide sequence
tcode Identify protein-coding regions using Fickett TESTCODE statistic
Command line arguments
Find programs by EDAM data
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
wossdata 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
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
wosstopic Find 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
|
