Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/acd/ggcskew.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GEMBASSY-1.0.3/acd/ggcskew.acd Fri Jun 26 05:19:29 2015 -0400 @@ -0,0 +1,85 @@ +application: ggcskew [ + documentation: "Calculates and plots the GC skew of the input sequence" + groups: "Nucleic:Composition" + embassy: "gembassy" + relations: "EDAM_topic:0157 Sequence composition analysis" + relations: "EDAM_operation:0377 Sequence composition calculation + (nucleic acid)" +] + +section: input [ + information: "Input section" + type: "page" +] + + seqall: sequence [ + parameter: "Y" + type: "nucleotide" + features: "Y" + relations: "EDAM_data:0849 Sequence record" + ] + +endsection: input + +section: advanced [ + information: "Advanced section" + type: "page" +] + + integer: window [ + information: "Window size to observe" + default: "10000" + ] + + integer: slide [ + information: "Window slide size" + default: "10000" + ] + + boolean: cumulative [ + information: "Include to calculate cumulative skew" + default: "N" + ] + + boolean: at [ + information: "Include for observing AT skew instead of GC skew" + default: "N" + ] + + boolean: purine [ + information: "Include for observing purine (AG/TC) skew" + default: "N" + ] + + boolean: keto [ + information: "Include for observing keto (TG/AC) skew" + default: "N" + ] + +endsection: advanced + +section: output [ + information: "Output section" + type: "page" +] + + toggle: plot [ + information: "Include to plot result" + default: "Y" + ] + + xygraph: graph [ + standard: "$(plot)" + gtitle: "ggcskew of $(sequence.name)" + ] + + outfile: outfile [ + standard: "@(!$(plot))" + nullok: "Y" + nulldefault: "$(plot)" + information: "Program compseq output file (optional)" + knowntype: "compseq output" + relations: "EDAM_data:3086 Nucleic acid sequence composition" + ] + +endsection: output