1application: infoseq [ 2 documentation: "Display basic information about sequences" 3 groups: "Data retrieval:Sequence data" 4 relations: "EDAM_topic:0090 Data search and retrieval" 5 relations: "EDAM_operation:1813 Sequence retrieval" 6] 7 8section: input [ 9 information: "Input section" 10 type: "page" 11] 12 13 seqall: sequence [ 14 parameter: "Y" 15 type: "gapany" 16 relations: "EDAM_data:0849 Sequence record" 17 ] 18 19endsection: input 20 21section: advanced [ 22 information: "Advanced section" 23 type: "page" 24] 25 26 boolean: columns [ 27 default: "Y" 28 information: "Print information in neat, aligned columns." 29 help: "Set this option on (Y) to print the sequence information 30 into neat, aligned columns in the output file. Alternatively, 31 leave it unset (N), in which case the information records will be 32 delimited by a character, which you may specify by using the 33 -delimiter option. In other words, if -columns is set on, the 34 -delimiter option is overriden." 35 relations: "EDAM_data:2527 Parameter" 36 ] 37 38 string: delimiter [ 39 default: "|" 40 information: "Delimiter of records in text output file" 41 help: "This string, which is usually a single character only, is 42 used to delimit individual records in the text output file. It 43 could be a space character, a tab character, a pipe character or 44 any other character or string." 45 knowntype: "output delimiter" 46 relations: "EDAM_data:2152 Rendering parameter" 47 ] 48 49endsection: advanced 50 51section: output [ 52 information: "Output section" 53 type: "page" 54] 55 56 outfile: outfile [ 57 additional: "Y" 58 default: "stdout" 59 knowntype: "infoseq output" 60 help: "If you enter the name of a file here then this program will 61 write the sequence details into that file." 62 relations: "EDAM_data:0855 Sequence metadata" 63 ] 64 65 boolean: html [ 66 additional: "Y" 67 default: "N" 68 information: "Format output as an HTML table" 69 outputmodifier: "Y" 70 relations: "EDAM_data:2527 Parameter" 71 ] 72 73 boolean: only [ 74 default: "N" 75 information: "Display the specified columns" 76 help: "This is a way of shortening the command line if you only 77 want a few things to be displayed. Instead of specifying: \ 78 '-nohead -noname -noacc -notype -nopgc -nodesc' \ 79 to get only the length output, you can specify \ 80 '-only -length'" 81 relations: "EDAM_data:2527 Parameter" 82 ] 83 84 boolean: heading [ 85 default: "Y" 86 information: "Display column headings" 87 relations: "EDAM_data:2527 Parameter" 88 ] 89 90 boolean: usa [ 91 default: "@(!$(only))" 92 information: "Display the USA of the sequence" 93 relations: "EDAM_data:2527 Parameter" 94 ] 95 96 boolean: database [ 97 default: "@(!$(only))" 98 information: "Display 'database' column" 99 relations: "EDAM_data:2527 Parameter" 100 ] 101 102 boolean: name [ 103 default: "@(!$(only))" 104 information: "Display 'name' column" 105 relations: "EDAM_data:2527 Parameter" 106 ] 107 108 boolean: accession [ 109 default: "@(!$(only))" 110 information: "Display 'accession' column" 111 relations: "EDAM_data:2527 Parameter" 112 ] 113 114 boolean: gi [ 115 default: "N" 116 information: "Display 'GI' column" 117 relations: "EDAM_data:2527 Parameter" 118 ] 119 120 boolean: seqversion [ 121 default: "N" 122 information: "Display 'version' column" 123 relations: "EDAM_data:2527 Parameter" 124 ] 125 126 boolean: type [ 127 default: "@(!$(only))" 128 information: "Display 'type' column" 129 relations: "EDAM_data:2527 Parameter" 130 ] 131 132 boolean: length [ 133 default: "@(!$(only))" 134 information: "Display 'length' column" 135 relations: "EDAM_data:2527 Parameter" 136 ] 137 138 boolean: pgc [ 139 default: "@(!$(only))" 140 information: "Display 'percent GC content' column" 141 relations: "EDAM_data:2527 Parameter" 142 ] 143 144 boolean: organism [ 145 default: "@(!$(only))" 146 information: "Display 'organism' column" 147 relations: "EDAM_data:2527 Parameter" 148 ] 149 150 boolean: description [ 151 default: "@(!$(only))" 152 information: "Display 'description' column" 153 relations: "EDAM_data:2527 Parameter" 154 ] 155 156endsection: output 157