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1 application: greporiter [
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2 documentation: "Gets the positions of replication origin and terminus"
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3 groups: "Nucleic:Composition"
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4 embassy: "gembassy"
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5 relations: "EDAM_topic:3073 Nucleic acid feature detection"
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6 relations: "EDAM_operation:0415 Nucleic acid feature prediction"
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7 ]
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8
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9 section: input [
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10 information: "Input section"
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11 type: "page"
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12 ]
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13
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14 seqall: sequence [
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15 parameter: "Y"
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16 type: "nucleotide"
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17 features: "Y"
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18 relations: "EDAM_data:0849 Sequence record"
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19 ]
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20
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21 endsection: input
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22
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23 section: advanced [
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24 information: "Advanced section"
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25 type: "page"
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26 ]
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27
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28 boolean: oriloc [
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29 information: "Include Oriloc for prediction"
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30 default: "N"
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31 ]
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32
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33 boolean: gcskew [
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34 information: "Include to use GC skew shift-point for prediction"
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35 default: "N"
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36 ]
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37
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38 integer: difthreshold [
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39 information: "Distance between the GC skew shift point and predicted dif
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40 site expressed as the precentage of genome size, used as a
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41 threshold to retrieve dif sequence from the database"
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42 default: "0"
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43 ]
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44
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45 boolean: dbonly [
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46 information: "Include to only use values available in databases and to
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47 suppress prediction"
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48 default: "N"
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49 ]
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50
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51 boolean: accid [
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52 information: "Include to use sequence accession ID as query"
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53 default: "N"
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54 ]
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55
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56 endsection: advanced
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57
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58 section: output [
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59 information: "Output section"
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60 type: "page"
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61 ]
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62
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63 outfile: outfile [
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64 parameter: "Y"
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65 relations: "EDAM_data:3127 Nucleic acid features (replication and
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66 recombination)"
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67 ]
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68
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69 endsection: output
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