--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rgenetics/rgQQ_code.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,50 @@
+# before running the qc, need to rename various output files
+#       <data format="html" name="html_file" />
+#       <data format="txt" name="log_file" parent="html_file" />
+#       <data format="tabular" name="marker_file" parent="html_file" />
+#       <data format="tabular" name="subject_file" parent="html_file" />
+
+from galaxy import datatypes,model
+import sys,string
+
+def get_columns( input ):
+    columns = []
+    elems = []
+    if input and input.metadata.columns:
+        ncols = input.metadata.columns
+        colnames = ['Col%d' % x for x in range(1,ncols+1)]
+        for i, line in enumerate( file ( input.file_name ) ):
+            valid = True
+            if line and not line.startswith( '#' ):
+                line = line.rstrip('\r\n')
+                elems = line.split( '\t' )
+
+                """
+                Since this tool requires users to select only those columns
+                that contain numerical values, we'll restrict the column select
+                list appropriately.
+                """
+                if len(elems) > 0:
+                    for col in range(len(elems)): # zero offset
+                       if i == 0: # header row
+                          colnames[col] = elems[col]
+                       else:
+                          val = elems[col]
+                          try:
+                              val = float(val)
+                              valid = True
+                          except:
+                              valid = False
+                       if valid:
+                            option = colnames[col]
+                            columns.append((option,str(col),False))
+                if len(columns) > 0:
+                    """
+                    We have our select list built, so we can break out of the outer most for loop
+                    """
+                    break
+            if i == 30:
+                break # Hopefully we never get here...
+    else:
+        columns = [('?','?',False),]
+    return columns