Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/acd/gbui.acd @ 0:8300eb051bea draft
Initial upload
| author | ktnyt |
|---|---|
| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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| -1:000000000000 | 0:8300eb051bea |
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| 1 application: gbui [ | |
| 2 documentation: "Calculates base usage indices for protein-coding sequences" | |
| 3 groups: "Nucleic:Codon usage" | |
| 4 embassy: "gembassy" | |
| 5 relations: "EDAM_topic:0157 Sequence composition analysis" | |
| 6 relations: "EDAM_operation:0236 Sequence composition calculation" | |
| 7 relations: "EDAM_operation:0377 Sequence composition calculation | |
| 8 (nucleic acid)" | |
| 9 ] | |
| 10 | |
| 11 section: input [ | |
| 12 information: "Input section" | |
| 13 type: "page" | |
| 14 ] | |
| 15 | |
| 16 seqall: sequence [ | |
| 17 parameter: "Y" | |
| 18 type: "nucleotide" | |
| 19 features: "Y" | |
| 20 relations: "EDAM_data:0849 Sequence record" | |
| 21 ] | |
| 22 | |
| 23 endsection: input | |
| 24 | |
| 25 section: advanced [ | |
| 26 information: "Advanced section" | |
| 27 type: "page" | |
| 28 ] | |
| 29 | |
| 30 boolean: translate [ | |
| 31 information: "Include when translating using standard codon table" | |
| 32 default: "N" | |
| 33 ] | |
| 34 | |
| 35 list: position [ | |
| 36 information: "Codon position" | |
| 37 values: "all: Assess overall base usage of the gene; | |
| 38 1: Assess base usage at 1st position of codons; | |
| 39 2: Assess base usage at 2nd position of codons; | |
| 40 3: Assess base usage at 3rd position of codons" | |
| 41 default: "all" | |
| 42 ] | |
| 43 | |
| 44 string: delkey [ | |
| 45 information: "Regular expression to delete key" | |
| 46 knowntype: "regular expression" | |
| 47 default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]" | |
| 48 ] | |
| 49 | |
| 50 boolean: accid [ | |
| 51 information: "Include to use sequence accession ID as query" | |
| 52 default: "N" | |
| 53 ] | |
| 54 | |
| 55 endsection: advanced | |
| 56 | |
| 57 section: output [ | |
| 58 information: "Output section" | |
| 59 type: "page" | |
| 60 ] | |
| 61 | |
| 62 outfile: outfile [ | |
| 63 parameter: "Y" | |
| 64 information: "Program compseq output file" | |
| 65 knowntype: "compseq output" | |
| 66 relations: "EDAM_data:3086 Nucleic acid sequence composition" | |
| 67 ] | |
| 68 | |
| 69 endsection: output |