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

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/acd/gfindoriter.acd	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,61 @@
+application: gfindoriter [
+  documentation: "Predicts the replication origin and terminus in bacterial genomes"
+  groups: "Nucleic:Composition"
+  embassy: "gembassy"
+  relations: "EDAM_topic:3073 Nucleic acid feature detection"
+  relations: "EDAM_operation:0415 Nucleic acid feature prediction"
+]
+
+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: "Number of windows to use for Fat Fourier Transform. Only active when -lowpass option is specified. Value must be the power of two"
+    default: "4096"
+  ]
+
+  boolean: purine [
+    information: "Use purine skew for calculation"
+    default: "N"
+  ]
+
+  boolean: keto [
+    information: "Use keto skew for calculation"
+    default: "N"
+  ]
+
+  integer: lowpass [
+    information: "Lowpass filter strength in percent. Typically 95 or 99 works best"
+    default: ""
+  ]
+
+endsection: advanced
+
+section: output [
+  information: "Output section"
+  type: "page"
+]
+
+  outfile: outfile [
+    parameter: "Y"
+    relations: "EDAM_data:3127 Nucleic acid features (replication and
+                recombination)"
+  ]
+
+endsection: output