diff GEMBASSY-1.0.3/acd/ggcwin.acd @ 0:8300eb051bea draft

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/acd/ggcwin.acd	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,75 @@
+application: ggcwin [
+  documentation: "Calculates and plots the GC content along the given genome"
+  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"
+  ]
+
+  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: "ggcwin 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