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

Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/acd/genret.acd	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,68 @@
+application: genret [
+  documentation: "Retrieves various gene features from genome flatfile"
+  groups: "Edit, Data retrieval, Feature tables"
+  embassy: "gembassy"
+  relations: "EDAM_topic:0160 Sequence sites and features"
+  relations: "EDAM_topic:0091 Data handling"
+  relations: "EDAM_operation:2422 Data retrieval"
+]
+
+section: input [
+  information: "Input section"
+  type: "page"
+]
+
+  seqall: sequence [
+    parameter: "Y"
+    type: "nucleotide"
+    features: "Y"
+    relations: "EDAM_data:0849 Sequence record"
+  ]
+
+  string: gene [
+    parameter: "Y"
+    information: "List of gene name(s) to report"
+    knowntype: "sequence id list"
+    default: "*"
+  ]
+
+  string: access [
+    parameter: "Y"
+    information: "Name of gene feature to access"
+    knowntype: "feature key"
+    word: "Y"
+  ]
+
+endsection: input
+
+section: advanced [
+  information: "Advanced section"
+  type: "page"
+]
+
+  string: argument [
+    information: "Extra arguments to pass to method"
+    knowntype: "string"
+    default: ""
+  ]
+
+  boolean: accid [
+    information: "Include to use sequence accession ID as query"
+    default: "N"
+  ]
+
+endsection: advanced
+
+section: output [
+  information: "Output section"
+  type: "page"
+]
+
+  outfile: outfile [
+    parameter: "Y"
+    extension: "$(access).genret"
+    information: "Sequence output file"
+    knowntype: "sequence data"
+  ]
+
+endsection: output