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>[-infile]<br>(Parameter 1)</td> 16<td>infile</td> 17<td>ABI sequencing trace file</td> 18<td>Input file</td> 19<td><b>Required</b></td> 20</tr> 21 22<tr bgcolor="#FFFFCC"> 23<td>[-outseq]<br>(Parameter 2)</td> 24<td>seqout</td> 25<td>Nucleotide sequence filename and optional format (output USA)</td> 26<td>Writeable sequence</td> 27<td><i><*></i>.<i>format</i></td> 28</tr> 29 30<tr bgcolor="#FFFFCC"> 31<td>-graph</td> 32<td>xygraph</td> 33<td>Graph type</td> 34<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> 35<td><i>EMBOSS_GRAPHICS</i> value, or x11</td> 36</tr> 37 38<tr bgcolor="#FFFFCC"> 39<th align="left" colspan=5>Additional (Optional) qualifiers</th> 40</tr> 41 42<tr bgcolor="#FFFFCC"> 43<td>-startbase</td> 44<td>integer</td> 45<td>First base to report or display</td> 46<td>Integer 0 or more</td> 47<td>0</td> 48</tr> 49 50<tr bgcolor="#FFFFCC"> 51<td>-endbase</td> 52<td>integer</td> 53<td>Last sequence base to report or display. If the default is set to zero then the value of this is taken as the maximum number of bases.</td> 54<td>Any integer value</td> 55<td>0</td> 56</tr> 57 58<tr bgcolor="#FFFFCC"> 59<td>-yticks</td> 60<td>boolean</td> 61<td>Display y-axis ticks</td> 62<td>Boolean value Yes/No</td> 63<td>No</td> 64</tr> 65 66<tr bgcolor="#FFFFCC"> 67<td>-[no]sequence</td> 68<td>boolean</td> 69<td>Display the sequence on the graph</td> 70<td>Boolean value Yes/No</td> 71<td>Yes</td> 72</tr> 73 74<tr bgcolor="#FFFFCC"> 75<td>-window</td> 76<td>integer</td> 77<td>Sequence display window size</td> 78<td>Any integer value</td> 79<td>40</td> 80</tr> 81 82<tr bgcolor="#FFFFCC"> 83<td>-bases</td> 84<td>string</td> 85<td>Base graphs to be displayed</td> 86<td>Any string, matching regular expression /[GATC]+/</td> 87<td>GATC</td> 88</tr> 89 90<tr bgcolor="#FFFFCC"> 91<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> 92</tr> 93 94<tr bgcolor="#FFFFCC"> 95<td>-separate</td> 96<td>boolean</td> 97<td>Separate the trace graphs for the 4 bases</td> 98<td>Boolean value Yes/No</td> 99<td>No</td> 100</tr> 101 102<tr bgcolor="#FFFFCC"> 103<th align="left" colspan=5>Associated qualifiers</th> 104</tr> 105 106<tr bgcolor="#FFFFCC"> 107<td align="left" colspan=5>"-outseq" associated seqout qualifiers 108</td> 109</tr> 110 111<tr bgcolor="#FFFFCC"> 112<td> -osformat2<br>-osformat_outseq</td> 113<td>string</td> 114<td>Output seq format</td> 115<td>Any string</td> 116<td> </td> 117</tr> 118 119<tr bgcolor="#FFFFCC"> 120<td> -osextension2<br>-osextension_outseq</td> 121<td>string</td> 122<td>File name extension</td> 123<td>Any string</td> 124<td> </td> 125</tr> 126 127<tr bgcolor="#FFFFCC"> 128<td> -osname2<br>-osname_outseq</td> 129<td>string</td> 130<td>Base file name</td> 131<td>Any string</td> 132<td> </td> 133</tr> 134 135<tr bgcolor="#FFFFCC"> 136<td> -osdirectory2<br>-osdirectory_outseq</td> 137<td>string</td> 138<td>Output directory</td> 139<td>Any string</td> 140<td> </td> 141</tr> 142 143<tr bgcolor="#FFFFCC"> 144<td> -osdbname2<br>-osdbname_outseq</td> 145<td>string</td> 146<td>Database name to add</td> 147<td>Any string</td> 148<td> </td> 149</tr> 150 151<tr bgcolor="#FFFFCC"> 152<td> -ossingle2<br>-ossingle_outseq</td> 153<td>boolean</td> 154<td>Separate file for each entry</td> 155<td>Boolean value Yes/No</td> 156<td>N</td> 157</tr> 158 159<tr bgcolor="#FFFFCC"> 160<td> -oufo2<br>-oufo_outseq</td> 161<td>string</td> 162<td>UFO features</td> 163<td>Any string</td> 164<td> </td> 165</tr> 166 167<tr bgcolor="#FFFFCC"> 168<td> -offormat2<br>-offormat_outseq</td> 169<td>string</td> 170<td>Features format</td> 171<td>Any string</td> 172<td> </td> 173</tr> 174 175<tr bgcolor="#FFFFCC"> 176<td> -ofname2<br>-ofname_outseq</td> 177<td>string</td> 178<td>Features file name</td> 179<td>Any string</td> 180<td> </td> 181</tr> 182 183<tr bgcolor="#FFFFCC"> 184<td> -ofdirectory2<br>-ofdirectory_outseq</td> 185<td>string</td> 186<td>Output directory</td> 187<td>Any string</td> 188<td> </td> 189</tr> 190 191<tr bgcolor="#FFFFCC"> 192<td align="left" colspan=5>"-graph" associated xygraph qualifiers 193</td> 194</tr> 195 196<tr bgcolor="#FFFFCC"> 197<td> -gprompt</td> 198<td>boolean</td> 199<td>Graph prompting</td> 200<td>Boolean value Yes/No</td> 201<td>N</td> 202</tr> 203 204<tr bgcolor="#FFFFCC"> 205<td> -gdesc</td> 206<td>string</td> 207<td>Graph description</td> 208<td>Any string</td> 209<td> </td> 210</tr> 211 212<tr bgcolor="#FFFFCC"> 213<td> -gtitle</td> 214<td>string</td> 215<td>Graph title</td> 216<td>Any string</td> 217<td> </td> 218</tr> 219 220<tr bgcolor="#FFFFCC"> 221<td> -gsubtitle</td> 222<td>string</td> 223<td>Graph subtitle</td> 224<td>Any string</td> 225<td> </td> 226</tr> 227 228<tr bgcolor="#FFFFCC"> 229<td> -gxtitle</td> 230<td>string</td> 231<td>Graph x axis title</td> 232<td>Any string</td> 233<td>Residue Position</td> 234</tr> 235 236<tr bgcolor="#FFFFCC"> 237<td> -gytitle</td> 238<td>string</td> 239<td>Graph y axis title</td> 240<td>Any string</td> 241<td> </td> 242</tr> 243 244<tr bgcolor="#FFFFCC"> 245<td> -goutfile</td> 246<td>string</td> 247<td>Output file for non interactive displays</td> 248<td>Any string</td> 249<td> </td> 250</tr> 251 252<tr bgcolor="#FFFFCC"> 253<td> -gdirectory</td> 254<td>string</td> 255<td>Output directory</td> 256<td>Any string</td> 257<td> </td> 258</tr> 259 260<tr bgcolor="#FFFFCC"> 261<th align="left" colspan=5>General qualifiers</th> 262</tr> 263 264<tr bgcolor="#FFFFCC"> 265<td> -auto</td> 266<td>boolean</td> 267<td>Turn off prompts</td> 268<td>Boolean value Yes/No</td> 269<td>N</td> 270</tr> 271 272<tr bgcolor="#FFFFCC"> 273<td> -stdout</td> 274<td>boolean</td> 275<td>Write first file to standard output</td> 276<td>Boolean value Yes/No</td> 277<td>N</td> 278</tr> 279 280<tr bgcolor="#FFFFCC"> 281<td> -filter</td> 282<td>boolean</td> 283<td>Read first file from standard input, write first file to standard output</td> 284<td>Boolean value Yes/No</td> 285<td>N</td> 286</tr> 287 288<tr bgcolor="#FFFFCC"> 289<td> -options</td> 290<td>boolean</td> 291<td>Prompt for standard and additional values</td> 292<td>Boolean value Yes/No</td> 293<td>N</td> 294</tr> 295 296<tr bgcolor="#FFFFCC"> 297<td> -debug</td> 298<td>boolean</td> 299<td>Write debug output to program.dbg</td> 300<td>Boolean value Yes/No</td> 301<td>N</td> 302</tr> 303 304<tr bgcolor="#FFFFCC"> 305<td> -verbose</td> 306<td>boolean</td> 307<td>Report some/full command line options</td> 308<td>Boolean value Yes/No</td> 309<td>Y</td> 310</tr> 311 312<tr bgcolor="#FFFFCC"> 313<td> -help</td> 314<td>boolean</td> 315<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td> 316<td>Boolean value Yes/No</td> 317<td>N</td> 318</tr> 319 320<tr bgcolor="#FFFFCC"> 321<td> -warning</td> 322<td>boolean</td> 323<td>Report warnings</td> 324<td>Boolean value Yes/No</td> 325<td>Y</td> 326</tr> 327 328<tr bgcolor="#FFFFCC"> 329<td> -error</td> 330<td>boolean</td> 331<td>Report errors</td> 332<td>Boolean value Yes/No</td> 333<td>Y</td> 334</tr> 335 336<tr bgcolor="#FFFFCC"> 337<td> -fatal</td> 338<td>boolean</td> 339<td>Report fatal errors</td> 340<td>Boolean value Yes/No</td> 341<td>Y</td> 342</tr> 343 344<tr bgcolor="#FFFFCC"> 345<td> -die</td> 346<td>boolean</td> 347<td>Report dying program messages</td> 348<td>Boolean value Yes/No</td> 349<td>Y</td> 350</tr> 351 352<tr bgcolor="#FFFFCC"> 353<td> -version</td> 354<td>boolean</td> 355<td>Report version number and exit</td> 356<td>Boolean value Yes/No</td> 357<td>N</td> 358</tr> 359 360</table> 361