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>[-cachefile]<br>(Parameter 1)</td> 16<td>outfile</td> 17<td>Server cache output file</td> 18<td>Output file</td> 19<td>server.$(servername)</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>-sequencesourcesonly</td> 28<td>boolean</td> 29<td>Display DAS sequence sources only</td> 30<td>Boolean value Yes/No</td> 31<td>No</td> 32</tr> 33 34<tr bgcolor="#FFFFCC"> 35<td>-outfile</td> 36<td>outfile</td> 37<td>Output file name</td> 38<td>Output file</td> 39<td>stdout</td> 40</tr> 41 42<tr bgcolor="#FFFFCC"> 43<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> 44</tr> 45 46<tr bgcolor="#FFFFCC"> 47<td>-host</td> 48<td>string</td> 49<td>DAS registry/server host location</td> 50<td>Any string</td> 51<td>www.dasregistry.org</td> 52</tr> 53 54<tr bgcolor="#FFFFCC"> 55<td>-path</td> 56<td>string</td> 57<td>DAS registry/server path on registry/server host</td> 58<td>Any string</td> 59<td>/das</td> 60</tr> 61 62<tr bgcolor="#FFFFCC"> 63<td>-port</td> 64<td>integer</td> 65<td>DAS registry/server port on registry/server host</td> 66<td>Any integer value</td> 67<td>80</td> 68</tr> 69 70<tr bgcolor="#FFFFCC"> 71<td>-servername</td> 72<td>string</td> 73<td>Name of a DAS server defined in EMBOSS resource files</td> 74<td>Any string</td> 75<td>das</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>"-outfile" associated outfile qualifiers 84</td> 85</tr> 86 87<tr bgcolor="#FFFFCC"> 88<td> -odirectory</td> 89<td>string</td> 90<td>Output directory</td> 91<td>Any string</td> 92<td> </td> 93</tr> 94 95<tr bgcolor="#FFFFCC"> 96<td align="left" colspan=5>"-cachefile" associated outfile qualifiers 97</td> 98</tr> 99 100<tr bgcolor="#FFFFCC"> 101<td> -odirectory1<br>-odirectory_cachefile</td> 102<td>string</td> 103<td>Output directory</td> 104<td>Any string</td> 105<td> </td> 106</tr> 107 108<tr bgcolor="#FFFFCC"> 109<th align="left" colspan=5>General qualifiers</th> 110</tr> 111 112<tr bgcolor="#FFFFCC"> 113<td> -auto</td> 114<td>boolean</td> 115<td>Turn off prompts</td> 116<td>Boolean value Yes/No</td> 117<td>N</td> 118</tr> 119 120<tr bgcolor="#FFFFCC"> 121<td> -stdout</td> 122<td>boolean</td> 123<td>Write first file to standard output</td> 124<td>Boolean value Yes/No</td> 125<td>N</td> 126</tr> 127 128<tr bgcolor="#FFFFCC"> 129<td> -filter</td> 130<td>boolean</td> 131<td>Read first file from standard input, write first file to standard output</td> 132<td>Boolean value Yes/No</td> 133<td>N</td> 134</tr> 135 136<tr bgcolor="#FFFFCC"> 137<td> -options</td> 138<td>boolean</td> 139<td>Prompt for standard and additional values</td> 140<td>Boolean value Yes/No</td> 141<td>N</td> 142</tr> 143 144<tr bgcolor="#FFFFCC"> 145<td> -debug</td> 146<td>boolean</td> 147<td>Write debug output to program.dbg</td> 148<td>Boolean value Yes/No</td> 149<td>N</td> 150</tr> 151 152<tr bgcolor="#FFFFCC"> 153<td> -verbose</td> 154<td>boolean</td> 155<td>Report some/full command line options</td> 156<td>Boolean value Yes/No</td> 157<td>Y</td> 158</tr> 159 160<tr bgcolor="#FFFFCC"> 161<td> -help</td> 162<td>boolean</td> 163<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td> 164<td>Boolean value Yes/No</td> 165<td>N</td> 166</tr> 167 168<tr bgcolor="#FFFFCC"> 169<td> -warning</td> 170<td>boolean</td> 171<td>Report warnings</td> 172<td>Boolean value Yes/No</td> 173<td>Y</td> 174</tr> 175 176<tr bgcolor="#FFFFCC"> 177<td> -error</td> 178<td>boolean</td> 179<td>Report errors</td> 180<td>Boolean value Yes/No</td> 181<td>Y</td> 182</tr> 183 184<tr bgcolor="#FFFFCC"> 185<td> -fatal</td> 186<td>boolean</td> 187<td>Report fatal errors</td> 188<td>Boolean value Yes/No</td> 189<td>Y</td> 190</tr> 191 192<tr bgcolor="#FFFFCC"> 193<td> -die</td> 194<td>boolean</td> 195<td>Report dying program messages</td> 196<td>Boolean value Yes/No</td> 197<td>Y</td> 198</tr> 199 200<tr bgcolor="#FFFFCC"> 201<td> -version</td> 202<td>boolean</td> 203<td>Report version number and exit</td> 204<td>Boolean value Yes/No</td> 205<td>N</td> 206</tr> 207 208</table> 209