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>[-sequences]<br>(Parameter 1)</td> 16<td>seqset</td> 17<td>File containing a sequence alignment</td> 18<td>Readable set of sequences</td> 19<td><b>Required</b></td> 20</tr> 21 22<tr bgcolor="#FFFFCC"> 23<td>-wordsize</td> 24<td>integer</td> 25<td>Word size</td> 26<td>Integer 2 or more</td> 27<td>6</td> 28</tr> 29 30<tr bgcolor="#FFFFCC"> 31<td>-outfeat</td> 32<td>featout</td> 33<td>Output features UFO</td> 34<td>Writeable feature table</td> 35<td><i>unknown.gff</i></td> 36</tr> 37 38<tr bgcolor="#FFFFCC"> 39<td>-graph</td> 40<td>graph</td> 41<td>Graph type</td> 42<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg</td> 43<td><i>EMBOSS_GRAPHICS</i> value, or x11</td> 44</tr> 45 46<tr bgcolor="#FFFFCC"> 47<th align="left" colspan=5>Additional (Optional) qualifiers</th> 48</tr> 49 50<tr bgcolor="#FFFFCC"> 51<td>-[no]boxit</td> 52<td>boolean</td> 53<td>Draw a box around each dotplot</td> 54<td>Boolean value Yes/No</td> 55<td>Yes</td> 56</tr> 57 58<tr bgcolor="#FFFFCC"> 59<td>-dumpfeat</td> 60<td>toggle</td> 61<td>Dump all matches as feature files</td> 62<td>Toggle value Yes/No</td> 63<td>No</td> 64</tr> 65 66<tr bgcolor="#FFFFCC"> 67<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> 68</tr> 69 70<tr bgcolor="#FFFFCC"> 71<td>-gap</td> 72<td>integer</td> 73<td>This specifies the size of the gap that is used to separate the individual dotplots in the display. The size is measured in residues, as displayed in the output.</td> 74<td>Integer 0 or more</td> 75<td>10</td> 76</tr> 77 78<tr bgcolor="#FFFFCC"> 79<th align="left" colspan=5>Associated qualifiers</th> 80</tr> 81 82<tr bgcolor="#FFFFCC"> 83<td align="left" colspan=5>"-sequences" associated seqset qualifiers 84</td> 85</tr> 86 87<tr bgcolor="#FFFFCC"> 88<td> -sbegin1<br>-sbegin_sequences</td> 89<td>integer</td> 90<td>Start of each sequence to be used</td> 91<td>Any integer value</td> 92<td>0</td> 93</tr> 94 95<tr bgcolor="#FFFFCC"> 96<td> -send1<br>-send_sequences</td> 97<td>integer</td> 98<td>End of each sequence to be used</td> 99<td>Any integer value</td> 100<td>0</td> 101</tr> 102 103<tr bgcolor="#FFFFCC"> 104<td> -sreverse1<br>-sreverse_sequences</td> 105<td>boolean</td> 106<td>Reverse (if DNA)</td> 107<td>Boolean value Yes/No</td> 108<td>N</td> 109</tr> 110 111<tr bgcolor="#FFFFCC"> 112<td> -sask1<br>-sask_sequences</td> 113<td>boolean</td> 114<td>Ask for begin/end/reverse</td> 115<td>Boolean value Yes/No</td> 116<td>N</td> 117</tr> 118 119<tr bgcolor="#FFFFCC"> 120<td> -snucleotide1<br>-snucleotide_sequences</td> 121<td>boolean</td> 122<td>Sequence is nucleotide</td> 123<td>Boolean value Yes/No</td> 124<td>N</td> 125</tr> 126 127<tr bgcolor="#FFFFCC"> 128<td> -sprotein1<br>-sprotein_sequences</td> 129<td>boolean</td> 130<td>Sequence is protein</td> 131<td>Boolean value Yes/No</td> 132<td>N</td> 133</tr> 134 135<tr bgcolor="#FFFFCC"> 136<td> -slower1<br>-slower_sequences</td> 137<td>boolean</td> 138<td>Make lower case</td> 139<td>Boolean value Yes/No</td> 140<td>N</td> 141</tr> 142 143<tr bgcolor="#FFFFCC"> 144<td> -supper1<br>-supper_sequences</td> 145<td>boolean</td> 146<td>Make upper case</td> 147<td>Boolean value Yes/No</td> 148<td>N</td> 149</tr> 150 151<tr bgcolor="#FFFFCC"> 152<td> -scircular1<br>-scircular_sequences</td> 153<td>boolean</td> 154<td>Sequence is circular</td> 155<td>Boolean value Yes/No</td> 156<td>N</td> 157</tr> 158 159<tr bgcolor="#FFFFCC"> 160<td> -squick1<br>-squick_sequences</td> 161<td>boolean</td> 162<td>Read id and sequence only</td> 163<td>Boolean value Yes/No</td> 164<td>N</td> 165</tr> 166 167<tr bgcolor="#FFFFCC"> 168<td> -sformat1<br>-sformat_sequences</td> 169<td>string</td> 170<td>Input sequence format</td> 171<td>Any string</td> 172<td> </td> 173</tr> 174 175<tr bgcolor="#FFFFCC"> 176<td> -iquery1<br>-iquery_sequences</td> 177<td>string</td> 178<td>Input query fields or ID list</td> 179<td>Any string</td> 180<td> </td> 181</tr> 182 183<tr bgcolor="#FFFFCC"> 184<td> -ioffset1<br>-ioffset_sequences</td> 185<td>integer</td> 186<td>Input start position offset</td> 187<td>Any integer value</td> 188<td>0</td> 189</tr> 190 191<tr bgcolor="#FFFFCC"> 192<td> -sdbname1<br>-sdbname_sequences</td> 193<td>string</td> 194<td>Database name</td> 195<td>Any string</td> 196<td> </td> 197</tr> 198 199<tr bgcolor="#FFFFCC"> 200<td> -sid1<br>-sid_sequences</td> 201<td>string</td> 202<td>Entryname</td> 203<td>Any string</td> 204<td> </td> 205</tr> 206 207<tr bgcolor="#FFFFCC"> 208<td> -ufo1<br>-ufo_sequences</td> 209<td>string</td> 210<td>UFO features</td> 211<td>Any string</td> 212<td> </td> 213</tr> 214 215<tr bgcolor="#FFFFCC"> 216<td> -fformat1<br>-fformat_sequences</td> 217<td>string</td> 218<td>Features format</td> 219<td>Any string</td> 220<td> </td> 221</tr> 222 223<tr bgcolor="#FFFFCC"> 224<td> -fopenfile1<br>-fopenfile_sequences</td> 225<td>string</td> 226<td>Features file name</td> 227<td>Any string</td> 228<td> </td> 229</tr> 230 231<tr bgcolor="#FFFFCC"> 232<td align="left" colspan=5>"-outfeat" associated featout qualifiers 233</td> 234</tr> 235 236<tr bgcolor="#FFFFCC"> 237<td> -offormat</td> 238<td>string</td> 239<td>Output feature format</td> 240<td>Any string</td> 241<td> </td> 242</tr> 243 244<tr bgcolor="#FFFFCC"> 245<td> -ofopenfile</td> 246<td>string</td> 247<td>Features file name</td> 248<td>Any string</td> 249<td> </td> 250</tr> 251 252<tr bgcolor="#FFFFCC"> 253<td> -ofextension</td> 254<td>string</td> 255<td>File name extension</td> 256<td>Any string</td> 257<td> </td> 258</tr> 259 260<tr bgcolor="#FFFFCC"> 261<td> -ofdirectory</td> 262<td>string</td> 263<td>Output directory</td> 264<td>Any string</td> 265<td> </td> 266</tr> 267 268<tr bgcolor="#FFFFCC"> 269<td> -ofname</td> 270<td>string</td> 271<td>Base file name</td> 272<td>Any string</td> 273<td> </td> 274</tr> 275 276<tr bgcolor="#FFFFCC"> 277<td> -ofsingle</td> 278<td>boolean</td> 279<td>Separate file for each entry</td> 280<td>Boolean value Yes/No</td> 281<td>N</td> 282</tr> 283 284<tr bgcolor="#FFFFCC"> 285<td align="left" colspan=5>"-graph" associated graph qualifiers 286</td> 287</tr> 288 289<tr bgcolor="#FFFFCC"> 290<td> -gprompt</td> 291<td>boolean</td> 292<td>Graph prompting</td> 293<td>Boolean value Yes/No</td> 294<td>N</td> 295</tr> 296 297<tr bgcolor="#FFFFCC"> 298<td> -gdesc</td> 299<td>string</td> 300<td>Graph description</td> 301<td>Any string</td> 302<td>Poly dotplot</td> 303</tr> 304 305<tr bgcolor="#FFFFCC"> 306<td> -gtitle</td> 307<td>string</td> 308<td>Graph title</td> 309<td>Any string</td> 310<td> </td> 311</tr> 312 313<tr bgcolor="#FFFFCC"> 314<td> -gsubtitle</td> 315<td>string</td> 316<td>Graph subtitle</td> 317<td>Any string</td> 318<td> </td> 319</tr> 320 321<tr bgcolor="#FFFFCC"> 322<td> -gxtitle</td> 323<td>string</td> 324<td>Graph x axis title</td> 325<td>Any string</td> 326<td> </td> 327</tr> 328 329<tr bgcolor="#FFFFCC"> 330<td> -gytitle</td> 331<td>string</td> 332<td>Graph y axis title</td> 333<td>Any string</td> 334<td> </td> 335</tr> 336 337<tr bgcolor="#FFFFCC"> 338<td> -goutfile</td> 339<td>string</td> 340<td>Output file for non interactive displays</td> 341<td>Any string</td> 342<td> </td> 343</tr> 344 345<tr bgcolor="#FFFFCC"> 346<td> -gdirectory</td> 347<td>string</td> 348<td>Output directory</td> 349<td>Any string</td> 350<td> </td> 351</tr> 352 353<tr bgcolor="#FFFFCC"> 354<th align="left" colspan=5>General qualifiers</th> 355</tr> 356 357<tr bgcolor="#FFFFCC"> 358<td> -auto</td> 359<td>boolean</td> 360<td>Turn off prompts</td> 361<td>Boolean value Yes/No</td> 362<td>N</td> 363</tr> 364 365<tr bgcolor="#FFFFCC"> 366<td> -stdout</td> 367<td>boolean</td> 368<td>Write first file to standard output</td> 369<td>Boolean value Yes/No</td> 370<td>N</td> 371</tr> 372 373<tr bgcolor="#FFFFCC"> 374<td> -filter</td> 375<td>boolean</td> 376<td>Read first file from standard input, write first file to standard output</td> 377<td>Boolean value Yes/No</td> 378<td>N</td> 379</tr> 380 381<tr bgcolor="#FFFFCC"> 382<td> -options</td> 383<td>boolean</td> 384<td>Prompt for standard and additional values</td> 385<td>Boolean value Yes/No</td> 386<td>N</td> 387</tr> 388 389<tr bgcolor="#FFFFCC"> 390<td> -debug</td> 391<td>boolean</td> 392<td>Write debug output to program.dbg</td> 393<td>Boolean value Yes/No</td> 394<td>N</td> 395</tr> 396 397<tr bgcolor="#FFFFCC"> 398<td> -verbose</td> 399<td>boolean</td> 400<td>Report some/full command line options</td> 401<td>Boolean value Yes/No</td> 402<td>Y</td> 403</tr> 404 405<tr bgcolor="#FFFFCC"> 406<td> -help</td> 407<td>boolean</td> 408<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td> 409<td>Boolean value Yes/No</td> 410<td>N</td> 411</tr> 412 413<tr bgcolor="#FFFFCC"> 414<td> -warning</td> 415<td>boolean</td> 416<td>Report warnings</td> 417<td>Boolean value Yes/No</td> 418<td>Y</td> 419</tr> 420 421<tr bgcolor="#FFFFCC"> 422<td> -error</td> 423<td>boolean</td> 424<td>Report errors</td> 425<td>Boolean value Yes/No</td> 426<td>Y</td> 427</tr> 428 429<tr bgcolor="#FFFFCC"> 430<td> -fatal</td> 431<td>boolean</td> 432<td>Report fatal errors</td> 433<td>Boolean value Yes/No</td> 434<td>Y</td> 435</tr> 436 437<tr bgcolor="#FFFFCC"> 438<td> -die</td> 439<td>boolean</td> 440<td>Report dying program messages</td> 441<td>Boolean value Yes/No</td> 442<td>Y</td> 443</tr> 444 445<tr bgcolor="#FFFFCC"> 446<td> -version</td> 447<td>boolean</td> 448<td>Report version number and exit</td> 449<td>Boolean value Yes/No</td> 450<td>N</td> 451</tr> 452 453</table> 454