Script that will run like a tool for each dataset generated. Is this in the right place? P.S. this stuff isn't final.

scripts/validate.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+
+"""
+Validate a dataset based on extension a metadata passed in on the
+command line.  Outputs a binhex'd representation of the exceptions.
+
+usage: %prog input output
+    -c, --cols=N,N,N,N: column metadata, in the case of GFF, BED, or intervals
+    -x, --ext=N: extension as understood by galaxy
+"""
+from cookbook import doc_optparse
+from galaxy import model
+from fileinput import FileInput
+from galaxy import util
+
+def main():
+    options, args = doc_optparse.parse( __doc__ )
+
+    try:
+        extension = options.ext
+    except:
+        doc_optparse.exception()
+
+    # create datatype
+    data = model.Dataset( extension=extension, id=int( args[0] ) )
+    data.file_path = "/home/ian/trunk/database/files/"
+    
+    if options.cols:
+        cols = options.cols.split(",")
+        data.metadata.chromCol = cols[0]
+        data.metadata.startCol = cols[1]
+        data.metadata.endCol = cols[2]
+        data.metadata.strandCol = cols[3]
+
+    errors = data.datatype.validate( data )
+    print util.object_to_string(errors)
+
+if __name__ == "__main__":
+    main()