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1 application: ggeneskew [
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2 documentation: "Calculates and plots the gene strand bias of the given genome"
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3 groups: "Nucleic:Composition"
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4 embassy: "gembassy"
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5 relations: "EDAM_topic:0157 Sequence composition analysis"
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6 relations: "EDAM_operation:0377 Sequence composition calculation
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7 (nucleic acid)"
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8 ]
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9
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10 section: input [
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11 information: "Input section"
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12 type: "page"
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13 ]
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14
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15 seqall: sequence [
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16 parameter: "Y"
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17 type: "nucleotide"
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18 features: "Y"
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19 relations: "EDAM_data:0849 Sequence record"
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20 ]
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21
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22 endsection: input
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23
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24 section: advanced [
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25 information: "Advanced section"
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26 type: "page"
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27 ]
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28
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29 integer: window [
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30 information: "Window size to observe"
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31 default: "10000"
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32 ]
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33
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34 integer: slide [
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35 information: "Window slide size"
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36 default: "10000"
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37 ]
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38
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39 boolean: cumulative [
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40 information: "Input 1 to calculate cumulative skew"
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41 default: "N"
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42 ]
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43
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44 selection: base [
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45 information: "Input 'gc', 'at', 'purine', or 'keto' for observing
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46 GC/AT/Purine/Keto skews"
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47 values: "none;gc;at;purine;keto"
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48 default: "none"
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49 ]
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50
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51 boolean: gctri [
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52 information: "Include to use only the third codon positions"
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53 default: "N"
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54 ]
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55
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56 boolean: accid [
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57 information: "Include to use sequence accession ID as query"
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58 default: "N"
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59 ]
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60
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61 endsection: advanced
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62
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63 section: output [
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64 information: "Output section"
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65 type: "page"
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66 ]
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67
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68 toggle: plot [
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69 information: "Include to plot result"
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70 default: "Y"
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71 ]
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72
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73 xygraph: graph [
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74 standard: "$(plot)"
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75 gtitle: "ggeneskew of $(sequence.name)"
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76 ]
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77
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78 outfile: outfile [
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79 standard: "@(!$(plot))"
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80 nullok: "Y"
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81 nulldefault: "$(plot)"
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82 information: "Program compseq output file (optional)"
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83 knowntype: "compseq output"
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84 relations: "EDAM_data:3086 Nucleic acid sequence composition"
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85 ]
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86
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87 endsection: output
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