Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/acd/ggeneskew.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: ggeneskew [ | |
| 2 documentation: "Calculates and plots the gene strand bias of the given genome" | |
| 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: window [ | |
| 30 information: "Window size to observe" | |
| 31 default: "10000" | |
| 32 ] | |
| 33 | |
| 34 integer: slide [ | |
| 35 information: "Window slide size" | |
| 36 default: "10000" | |
| 37 ] | |
| 38 | |
| 39 boolean: cumulative [ | |
| 40 information: "Input 1 to calculate cumulative skew" | |
| 41 default: "N" | |
| 42 ] | |
| 43 | |
| 44 selection: base [ | |
| 45 information: "Input 'gc', 'at', 'purine', or 'keto' for observing | |
| 46 GC/AT/Purine/Keto skews" | |
| 47 values: "none;gc;at;purine;keto" | |
| 48 default: "none" | |
| 49 ] | |
| 50 | |
| 51 boolean: gctri [ | |
| 52 information: "Include to use only the third codon positions" | |
| 53 default: "N" | |
| 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 toggle: plot [ | |
| 69 information: "Include to plot result" | |
| 70 default: "Y" | |
| 71 ] | |
| 72 | |
| 73 xygraph: graph [ | |
| 74 standard: "$(plot)" | |
| 75 gtitle: "ggeneskew of $(sequence.name)" | |
| 76 ] | |
| 77 | |
| 78 outfile: outfile [ | |
| 79 standard: "@(!$(plot))" | |
| 80 nullok: "Y" | |
| 81 nulldefault: "$(plot)" | |
| 82 information: "Program compseq output file (optional)" | |
| 83 knowntype: "compseq output" | |
| 84 relations: "EDAM_data:3086 Nucleic acid sequence composition" | |
| 85 ] | |
| 86 | |
| 87 endsection: output |