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

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/acd/goligomersearch.acd	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,59 @@
+application: goligomersearch [
+  documentation: "Searches oligomers in given 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"
+  ]
+
+  string: oligomer [
+    parameter: "Y"
+    knowntype: "nucleotide codes"
+    information: "Oligomer to search"
+  ]
+
+endsection: input
+
+section: advanced [
+  information: "Advanced section"
+  type: "page"
+]
+
+  selection: return [
+    information: "'position' to return list of positions where oligomers are
+                  found, 'oligo' to return list of oligomers found ordered by
+                  positions, 'both' to return a hash with positions as keys and
+                  oligomers as values, 'distribution' to return four values
+                  about the distribution of given oligomer"
+    values: "position;oligo;both;distribution"
+    default: "position"
+  ]
+
+endsection: advanced
+
+section: output [
+  information: "Output section"
+  type: "page"
+]
+
+  outfile: outfile [
+    parameter: "Y"
+    information: "Program compseq output file"
+    knowntype: "compseq output"
+    relations: "EDAM_data:3086 Nucleic acid sequence composition"
+  ]
+
+endsection: output