1<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
2<tr bgcolor="#FFFFCC">
3<th align="left">Qualifier</th>
4<th align="left">Type</th>
5<th align="left">Description</th>
6<th align="left">Allowed values</th>
7<th align="left">Default</th>
8</tr>
9
10<tr bgcolor="#FFFFCC">
11<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
12</tr>
13
14<tr bgcolor="#FFFFCC">
15<td>[-identifier]<br>(Parameter 1)</td>
16<td>string</td>
17<td>Identifier(s) to search for in ontology</td>
18<td>Any string</td>
19<td>&nbsp;</td>
20</tr>
21
22<tr bgcolor="#FFFFCC">
23<th align="left" colspan=5>Additional (Optional) qualifiers</th>
24</tr>
25
26<tr bgcolor="#FFFFCC">
27<td>-explode</td>
28<td>boolean</td>
29<td>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'.</td>
30<td>Boolean value Yes/No</td>
31<td>No</td>
32</tr>
33
34<tr bgcolor="#FFFFCC">
35<td>-showkeywords</td>
36<td>boolean</td>
37<td>Show keywords with program documentation</td>
38<td>Boolean value Yes/No</td>
39<td>No</td>
40</tr>
41
42<tr bgcolor="#FFFFCC">
43<td>-outfile</td>
44<td>outfile</td>
45<td>Tool metadata output file</td>
46<td>Output file</td>
47<td>stdout</td>
48</tr>
49
50<tr bgcolor="#FFFFCC">
51<td>-html</td>
52<td>toggle</td>
53<td>If you are sending the output to a file, this will format it for displaying as a table in a WWW document.</td>
54<td>Toggle value Yes/No</td>
55<td>No</td>
56</tr>
57
58<tr bgcolor="#FFFFCC">
59<td>-groups</td>
60<td>boolean</td>
61<td>If you use this option, then only the group names will be output to the file</td>
62<td>Boolean value Yes/No</td>
63<td>No</td>
64</tr>
65
66<tr bgcolor="#FFFFCC">
67<td>-alphabetic</td>
68<td>boolean</td>
69<td>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.</td>
70<td>Boolean value Yes/No</td>
71<td>No</td>
72</tr>
73
74<tr bgcolor="#FFFFCC">
75<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
76</tr>
77
78<tr bgcolor="#FFFFCC">
79<td>-sensitive</td>
80<td>boolean</td>
81<td>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.</td>
82<td>Boolean value Yes/No</td>
83<td>No</td>
84</tr>
85
86<tr bgcolor="#FFFFCC">
87<td>-[no]subclasses</td>
88<td>boolean</td>
89<td>Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type.</td>
90<td>Boolean value Yes/No</td>
91<td>Yes</td>
92</tr>
93
94<tr bgcolor="#FFFFCC">
95<td>-obsolete</td>
96<td>boolean</td>
97<td>The default behaviour is to not use or return obsolete terms. This option if set will include all terms.</td>
98<td>Boolean value Yes/No</td>
99<td>No</td>
100</tr>
101
102<tr bgcolor="#FFFFCC">
103<td>-[no]emboss</td>
104<td>boolean</td>
105<td>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</td>
106<td>Boolean value Yes/No</td>
107<td>Yes</td>
108</tr>
109
110<tr bgcolor="#FFFFCC">
111<td>-[no]embassy</td>
112<td>boolean</td>
113<td>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</td>
114<td>Boolean value Yes/No</td>
115<td>Yes</td>
116</tr>
117
118<tr bgcolor="#FFFFCC">
119<td>-showembassy</td>
120<td>string</td>
121<td>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</td>
122<td>Any string</td>
123<td>&nbsp;</td>
124</tr>
125
126<tr bgcolor="#FFFFCC">
127<td>-colon</td>
128<td>boolean</td>
129<td>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.</td>
130<td>Boolean value Yes/No</td>
131<td>No</td>
132</tr>
133
134<tr bgcolor="#FFFFCC">
135<td>-gui</td>
136<td>boolean</td>
137<td>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</td>
138<td>Boolean value Yes/No</td>
139<td>No</td>
140</tr>
141
142<tr bgcolor="#FFFFCC">
143<th align="left" colspan=5>Associated qualifiers</th>
144</tr>
145
146<tr bgcolor="#FFFFCC">
147<td align="left" colspan=5>"-outfile" associated outfile qualifiers
148</td>
149</tr>
150
151<tr bgcolor="#FFFFCC">
152<td> -odirectory</td>
153<td>string</td>
154<td>Output directory</td>
155<td>Any string</td>
156<td>&nbsp;</td>
157</tr>
158
159<tr bgcolor="#FFFFCC">
160<th align="left" colspan=5>General qualifiers</th>
161</tr>
162
163<tr bgcolor="#FFFFCC">
164<td> -auto</td>
165<td>boolean</td>
166<td>Turn off prompts</td>
167<td>Boolean value Yes/No</td>
168<td>N</td>
169</tr>
170
171<tr bgcolor="#FFFFCC">
172<td> -stdout</td>
173<td>boolean</td>
174<td>Write first file to standard output</td>
175<td>Boolean value Yes/No</td>
176<td>N</td>
177</tr>
178
179<tr bgcolor="#FFFFCC">
180<td> -filter</td>
181<td>boolean</td>
182<td>Read first file from standard input, write first file to standard output</td>
183<td>Boolean value Yes/No</td>
184<td>N</td>
185</tr>
186
187<tr bgcolor="#FFFFCC">
188<td> -options</td>
189<td>boolean</td>
190<td>Prompt for standard and additional values</td>
191<td>Boolean value Yes/No</td>
192<td>N</td>
193</tr>
194
195<tr bgcolor="#FFFFCC">
196<td> -debug</td>
197<td>boolean</td>
198<td>Write debug output to program.dbg</td>
199<td>Boolean value Yes/No</td>
200<td>N</td>
201</tr>
202
203<tr bgcolor="#FFFFCC">
204<td> -verbose</td>
205<td>boolean</td>
206<td>Report some/full command line options</td>
207<td>Boolean value Yes/No</td>
208<td>Y</td>
209</tr>
210
211<tr bgcolor="#FFFFCC">
212<td> -help</td>
213<td>boolean</td>
214<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
215<td>Boolean value Yes/No</td>
216<td>N</td>
217</tr>
218
219<tr bgcolor="#FFFFCC">
220<td> -warning</td>
221<td>boolean</td>
222<td>Report warnings</td>
223<td>Boolean value Yes/No</td>
224<td>Y</td>
225</tr>
226
227<tr bgcolor="#FFFFCC">
228<td> -error</td>
229<td>boolean</td>
230<td>Report errors</td>
231<td>Boolean value Yes/No</td>
232<td>Y</td>
233</tr>
234
235<tr bgcolor="#FFFFCC">
236<td> -fatal</td>
237<td>boolean</td>
238<td>Report fatal errors</td>
239<td>Boolean value Yes/No</td>
240<td>Y</td>
241</tr>
242
243<tr bgcolor="#FFFFCC">
244<td> -die</td>
245<td>boolean</td>
246<td>Report dying program messages</td>
247<td>Boolean value Yes/No</td>
248<td>Y</td>
249</tr>
250
251<tr bgcolor="#FFFFCC">
252<td> -version</td>
253<td>boolean</td>
254<td>Report version number and exit</td>
255<td>Boolean value Yes/No</td>
256<td>N</td>
257</tr>
258
259</table>
260