Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/acd/gbaseentropy.acd @ 0:8300eb051bea draft
Initial upload
| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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| -1:000000000000 | 0:8300eb051bea |
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| 1 application: gbaseentropy [ | |
| 2 documentation: "Calculates and graphs the sequence conservation | |
| 3 using Shanon uncertainty (entropy)" | |
| 4 groups: "Nucleic:Composition" | |
| 5 embassy: "gembassy" | |
| 6 relations: "EDAM_topic:0160 Sequence sites and features" | |
| 7 relations: "EDAM_operation:0253 Feature prediction" | |
| 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 selection: position [ | |
| 30 information: "Either 'start' (around start codon) or 'end' | |
| 31 (around stop codon) to create the PWM" | |
| 32 values: "start;end" | |
| 33 default: "start" | |
| 34 ] | |
| 35 | |
| 36 integer: patlen [ | |
| 37 information: "Length of oligomer to count" | |
| 38 default: "3" | |
| 39 ] | |
| 40 | |
| 41 integer: upstream [ | |
| 42 information: "Length upstream of specified position to create PWM" | |
| 43 default: "30" | |
| 44 ] | |
| 45 | |
| 46 integer: downstream [ | |
| 47 information: "Length downstream of specified position to create PWM" | |
| 48 default: "30" | |
| 49 ] | |
| 50 | |
| 51 boolean: accid [ | |
| 52 information: "Include to use sequence accession ID as query" | |
| 53 default: "N" | |
| 54 ] | |
| 55 | |
| 56 endsection: advanced | |
| 57 | |
| 58 section: output [ | |
| 59 information: "Output section" | |
| 60 type: "page" | |
| 61 ] | |
| 62 | |
| 63 toggle: plot [ | |
| 64 information: "Include to plot result" | |
| 65 default: "Y" | |
| 66 ] | |
| 67 | |
| 68 xygraph: graph [ | |
| 69 standard: "$(plot)" | |
| 70 gtitle: "gbaseentropy of $(sequence.name)" | |
| 71 relations: "EDAM_data:2166 Sequence compisition plot" | |
| 72 ] | |
| 73 | |
| 74 outfile: outfile [ | |
| 75 standard: "@(!$(plot))" | |
| 76 nullok: "Y" | |
| 77 nulldefault: "$(plot)" | |
| 78 information: "Program compseq output file (optional)" | |
| 79 knowntype: "compseq output" | |
| 80 relations: "EDAM_data:3086 Nucleic acid sequence composition" | |
| 81 ] | |
| 82 | |
| 83 endsection: output |