Enhancements to the way dynamic_options work in order to enable tools using dynemic_options to function in workdflow.

We're still supporting the current dynamic_options functionality.  This is a first pass and will be cleaned up as we continue to evolve more tools to use this new approach.
Within tool configs, SelectToolParameter types now include a <select_options> tag set.  Several tools have been altered to use this new approach.  Other tools we enhanced to
use the ColumnListParameter type.

tools/data_source/encode_import_code.py

@@ -1,103 +1,9 @@
-#build list of available data
 import os, sys
-encode_sets= {}
 
-try:
-    for line in open( "/depot/data2/galaxy/encode_datasets.loc" ):
-        if line[0:1] == "#" : continue
-        
-        fields = line.split('\t')
-        #read each line, if not enough fields, go to next line
-        try:
-            encode_group = fields[0]
-            build = fields[1]
-            description = fields[2]
-            uid = fields[3]
-            path = fields[4].replace("\n","").replace("\r","")
-            try:
-                file_type = fields[5].replace("\n","").replace("\r","")
-            except:
-                file_type = "bed"
-            #will remove this later, when galaxy can handle gff files
-            if file_type != "bed":
-                continue
-            #verify that file exists before making it an option
-            if not os.path.isfile(path):
-                continue
-        except:
-            continue
-        #check if group is initialized, if not inititalize
-        try:
-            temp = encode_sets[encode_group]
-        except:
-            encode_sets[encode_group] = {}
-        #add data to group in proper build
-        try:
-            encode_sets[encode_group][build].append((description, uid, False))
-        except:
-            encode_sets[encode_group][build]=[]
-            encode_sets[encode_group][build].append((description, uid, False))
-            
-    #Order by description and date, highest date on top and bold
-    for group in encode_sets:
-        for build in encode_sets[group]:
-            ordered_build = []
-            for description, uid, selected in encode_sets[group][build]:
-                item = {}
-                item['date']=0
-                item['description'] = ""
-                item['uid']=uid
-                item['selected']=selected
-                item['partitioned']=False
-                
-                if description[-21:]=='[gencode_partitioned]':
-                    item['date'] = description[-31:-23]
-                    item['description'] = description[0:-32]
-                    item['partitioned']=True
-                else:
-                    item['date'] = description[-9:-1]
-                    item['description'] = description[0:-10]
-                    
-                for i in range(len(ordered_build)):
-                    ordered_description, ordered_uid, ordered_selected, ordered_item = ordered_build[i]
-                    if item['description'] < ordered_item['description']:
-                        ordered_build.insert(i, (description, uid, selected, item) )
-                        break
-                    if item['description'] == ordered_item['description'] and item['partitioned'] == ordered_item['partitioned']:
-                        if int(item['date']) > int(ordered_item['date']):
-                            ordered_build.insert(i, (description, uid, selected, item) )
-                            break
-                else:
-                    ordered_build.append( (description, uid, selected, item) )
-            
-            last_desc = None
-            last_partitioned = None
-            for i in range(len(ordered_build)) :
-                description, uid, selected, item = ordered_build[i]
-                if item['partitioned'] != last_partitioned or last_desc != item['description']:
-                    last_desc = item['description']
-                    description = "<b>"+description+"</b>"
-                else:
-                    last_desc = item['description']
-                last_partitioned = item['partitioned']
-                encode_sets[group][build][i] = (description, uid, selected)
-                    
-except Exception, exc:
-    print >>sys.stdout, 'encode_import_code.py initialization error -> %s' % exc 
-
-#return available datasets for group and build, set None option as selected for hg16
-def get_available_data( encode_group, build ):
-    try:
-        available_options = encode_sets[encode_group][build][0:]
-    except:
-        available_options = []
-    if len(available_options) < 1:
-        available_options.append(('No data available for this build','None',True))
-    return available_options
-
-#post processing, set build for data and add additional data to history
 from galaxy import datatypes, config, jobs 
 from shutil import copyfile
+
+#post processing, set build for data and add additional data to history
 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
     history = out_data.items()[0][1].history
     if history == None: