Fixes for column_maker and filtering tool to use new approach for handling metadata in the tool params - functional tests should now pass.

tools/stats/column_maker.py

@@ -19,7 +19,9 @@ expr = sys.argv[3]
 round = sys.argv[4] 
 try:
     in_columns = int( sys.argv[5] )
-    in_column_types = sys.argv[6].split( ',' )
+    # in_column_types is passed as a string that looks something like:
+    # "[u'str', u'int', u'int', u'str', u'int', u'str']"
+    in_column_types = sys.argv[6].strip( '[' ).strip( ']' ).replace( 'u', '' ).replace( "'", '' ).split( ',' )
 except:
     stop_err( "Data does not appear to be tabular.  This tool can only be used with tab-delimited data." )
 
@@ -42,12 +44,12 @@ cols, type_casts = [], []
 for col in range( 1, in_columns + 1 ):
     col_name = "c%d" % col
     cols.append( col_name )
-    col_type = in_column_types[ col - 1 ]
+    col_type = in_column_types[ col - 1 ].strip()
     if round == 'no' and col_type == 'int':
         col_type = 'float'
     type_cast = "%s(%s)" % ( col_type, col_name )
     type_casts.append( type_cast )
-        
+
 col_str = ', '.join( cols )    # 'c1, c2, c3, c4'
 type_cast_str = ', '.join( type_casts )  # 'str(c1), int(c2), int(c3), str(c4)'
 assign = "%s = line.split( '\\t' )" % col_str

tools/stats/column_maker.xml

@@ -1,7 +1,7 @@
-<tool id="Add a column1" name="Compute">
+<tool id="Add_a_column1" name="Compute">
   <description>an expression on every row</description>
   <command interpreter="python">
-    column_maker.py $input $out_file1 "$cond" $round $input_columns $input_column_types
+    column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}"
   </command>
   <inputs>
     <param name="cond" size="40" type="text" value="c3-c2" label="Add expression"/>

tools/stats/filtering.py

@@ -26,7 +26,9 @@ out_fname = sys.argv[2]
 cond_text = sys.argv[3]
 try:
     in_columns = int( sys.argv[4] )
-    in_column_types = sys.argv[5].split( ',' )
+    # in_column_types is passed as a string that looks something like:
+    # "[u'str', u'int', u'int', u'str', u'int', u'str']"
+    in_column_types = sys.argv[5].strip( '[' ).strip( ']' ).replace( 'u', '' ).replace( "'", '' ).split( ',' )
 except:
     stop_err( "Data does not appear to be tabular.  This tool can only be used with tab-delimited data." )
 

tools/stats/filtering.xml

@@ -1,7 +1,7 @@
 <tool id="Filter1" name="Filter">
   <description>data on any column using simple expressions</description>
   <command interpreter="python">
-    filtering.py $input $out_file1 "$cond" $input_columns $input_column_types
+    filtering.py $input $out_file1 "$cond" ${input.metadata.columns} "${input.metadata.column_types}"
   </command>
   <inputs>
     <param format="tabular" name="input" type="data" label="Filter" help="Query missing? See TIP below."/>