Remove imports of the sets module, set has been a standard type since 2.4. There are more in tools, but they check for the existence of set() first, so will not raise a warning.

tools/indels/indel_analysis.py

@@ -10,7 +10,7 @@ usage: %prog [options] [input3 sum3[ input4 sum4[ input5 sum5[...]]]]
    -D, --out_del=D: The interval output file showing deletions
 """
 
-import re, sets, sys
+import re, sys
 from galaxy import eggs
 import pkg_resources; pkg_resources.require( "bx-python" )
 from bx.cookbook import doc_optparse
@@ -130,7 +130,7 @@ def __main__():
         poses = mis_matches[ chrom ].keys()
         poses.extend( indels[ chrom ][ 'D' ].keys() )
         poses.extend( indels[ chrom ][ 'I' ].keys() )
-        poses = list( sets.Set( poses ) )
+        poses = list( set( poses ) )
         for pos in poses:
             # all reads touching this particular position
             freqs[ chrom ][ pos ] = {}

tools/samtools/sam_merge_code.py

@@ -1,9 +1,8 @@
-import sets
 from galaxy.tools.parameters import DataToolParameter
 
 def validate_input( trans, error_map, param_values, page_param_map ):
-    dbkeys = sets.Set()
-    data_param_names = sets.Set()
+    dbkeys = set()
+    data_param_names = set()
     data_params = 0
     for name, param in page_param_map.iteritems():
         if isinstance( param, DataToolParameter ):
@@ -32,4 +31,4 @@ def validate_input( trans, error_map, param_values, page_param_map ):
                 "this dataset is linked to build '%s'" % param_values[name].dbkey
     if data_params != len(data_param_names):
         for name in data_param_names:
-            error_map[name] = "A dataset of the appropriate type is required"
+            error_map[name] = "A dataset of the appropriate type is required"