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