Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/acd/gbasezvalue.acd @ 2:8947fca5f715 draft default tip
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| author | ktnyt |
|---|---|
| date | Fri, 26 Jun 2015 05:21:44 -0400 |
| parents | 84a17b3fad1f |
| children |
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| 1:84a17b3fad1f | 2:8947fca5f715 |
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| 1 application: gbasezvalue [ | |
| 2 documentation: "Extracts conserved oligomers per position using Z-score" | |
| 3 groups: "Nucleic:Composition" | |
| 4 embassy: "gembassy" | |
| 5 relations: "EDAM_topic:0157 Sequence composition analysis" | |
| 6 relations: "EDAM_operation:0377 Sequence composition calculation | |
| 7 (nucleic acid)" | |
| 8 ] | |
| 9 | |
| 10 section: input [ | |
| 11 information: "Input section" | |
| 12 type: "page" | |
| 13 ] | |
| 14 | |
| 15 seqall: sequence [ | |
| 16 parameter: "Y" | |
| 17 type: "nucleotide" | |
| 18 features: "Y" | |
| 19 relations: "EDAM_data:0849 Sequence record" | |
| 20 ] | |
| 21 | |
| 22 endsection: input | |
| 23 | |
| 24 section: advanced [ | |
| 25 information: "Advanced section" | |
| 26 type: "page" | |
| 27 ] | |
| 28 | |
| 29 integer: limit [ | |
| 30 information: "Rank threshold for showing the conserved oligomer" | |
| 31 default: "5" | |
| 32 ] | |
| 33 | |
| 34 selection: position [ | |
| 35 information: "Either 'start' (around start codon) or 'end' | |
| 36 (around stop codon) to create the PWM" | |
| 37 values: "start;end" | |
| 38 default: "start" | |
| 39 ] | |
| 40 | |
| 41 integer: patlen [ | |
| 42 information: "Length of oligomer to count" | |
| 43 default: "3" | |
| 44 ] | |
| 45 | |
| 46 integer: upstream [ | |
| 47 information: "Length upstream of specified position to create PWM" | |
| 48 default: "30" | |
| 49 ] | |
| 50 | |
| 51 integer: downstream [ | |
| 52 information: "Length downstream of specified position to create PWM" | |
| 53 default: "30" | |
| 54 ] | |
| 55 | |
| 56 boolean: accid [ | |
| 57 information: "Include to use sequence accession ID as query" | |
| 58 default: "N" | |
| 59 ] | |
| 60 | |
| 61 endsection: advanced | |
| 62 | |
| 63 section: output [ | |
| 64 information: "Output section" | |
| 65 type: "page" | |
| 66 ] | |
| 67 | |
| 68 outfile: outfile [ | |
| 69 parameter: "Y" | |
| 70 information: "Program compseq output file (optional)" | |
| 71 knowntype: "compseq output" | |
| 72 relations: "EDAM_data:3086 Nucleic acid sequence composition" | |
| 73 ] | |
| 74 | |
| 75 endsection: output |