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1 application: ggcsi [
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2 documentation: "GC Skew Index: an index for strand-specific mutational bias"
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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 selection: gcsi [
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30 information: "GCSI version to use"
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31 values: "1;2"
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32 default: "2"
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33 ]
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34
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35 integer: window [
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36 information: "Number of windows. Must be a power of 2"
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37 default: "4096"
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38 ]
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39
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40 boolean: purine [
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41 information: "Use purine skew for calculation"
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42 default: "N"
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43 ]
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44
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45 boolean: keto [
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46 information: "Use keto skew for calculation"
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47 default: "N"
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48 ]
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49
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50 boolean: at [
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51 information: "Use AT skew for calculation"
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52 default: "N"
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53 ]
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54
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55 boolean: pval [
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56 information: "Calculate p-value when GCSI version 2 is selected"
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57 default: "N"
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58 ]
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59
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60 endsection: advanced
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61
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62 section: output [
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63 information: "Output section"
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64 type: "page"
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65 ]
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66
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67 outfile: outfile [
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68 parameter: "Y"
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69 information: "Program compseq output file"
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70 knowntype: "compseq output"
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71 relations: "EDAM_data:3086 Nucleic acid sequence composition"
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72 ]
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73
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74 endsection: output
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