--- a/hubArchiveCreator.py	Thu Jul 21 05:58:51 2016 -0400
+++ b/hubArchiveCreator.py	Wed Jul 27 10:10:49 2016 -0400
@@ -82,13 +82,16 @@
     input_fasta_file_name = sanitize_name_input(array_inputs_reference_genome["name"])
     genome_name = sanitize_name_input(args.genome_name)
 
-    reference_genome = Fasta(array_inputs_reference_genome["false_path"],
+    reference_genome = Fasta(input_fasta_file,
                              input_fasta_file_name, genome_name)
 
     user_email = args.user_email
 
-    # TODO: Add array for each input because we can add multiple -b for example + filter the data associated
 
+    # TODO: Use a class to have a better management of the structure of these inputs
+    # These inputs are populated in the Galaxy Wrapper xml and are in this format:
+    # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}]
+    # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}
     array_inputs_gff3 = args.gff3
     array_inputs_bed_simple_repeats = args.bedSimpleRepeats
     array_inputs_bed_generic = args.bed
@@ -117,31 +120,14 @@
 
     all_datatype_dictionary = {}
 
-    datatype_parameters = (inputs_data, all_datatype_dictionary)
-
-    # Process Augustus
-    if array_inputs_gff3:
-        create_ordered_datatype_objects(Gff3, array_inputs_gff3, *datatype_parameters)
-
-    # Process Bed simple repeats
-    if array_inputs_bed_simple_repeats:
-        create_ordered_datatype_objects(BedSimpleRepeats, array_inputs_bed_simple_repeats, *datatype_parameters)
-
-    # Process Bed
-    if array_inputs_bed_generic:
-        create_ordered_datatype_objects(Bed, array_inputs_bed_generic, *datatype_parameters)
-
-    # Process GTF
-    if array_inputs_gtf:
-        create_ordered_datatype_objects(Gtf, array_inputs_gtf, *datatype_parameters)
-
-    # Process Bam
-    if array_inputs_bam:
-        create_ordered_datatype_objects(Bam, array_inputs_bam, *datatype_parameters)
-
-    # Process BigWig
-    if array_inputs_bigwig:
-        create_ordered_datatype_objects(BigWig, array_inputs_bigwig, *datatype_parameters)
+    for (inputs, datatype_class) in [(array_inputs_gff3, Gff3),
+                         (array_inputs_bed_simple_repeats, BedSimpleRepeats),
+                         (array_inputs_bed_generic, Bed),
+                         (array_inputs_gtf, Gtf),
+                         (array_inputs_bam, Bam),
+                         (array_inputs_bigwig, BigWig)]:
+        if inputs:
+            all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))
 
     # Create Ordered Dictionary to add the tracks in the tool form order
     all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)
@@ -155,13 +141,19 @@
     # We terminate le process and so create a HTML file summarizing all the files
     trackHub.terminate()
 
+    print "\t"
+    print "--------------"
+    print "Well done guys! Your data are ready to be displayed in UCSC Track Hub."
+
     sys.exit(0)
 
+
 def sanitize_name_input(string_to_sanitize):
         return string_to_sanitize \
             .replace("/", "_") \
             .replace(" ", "_")
 
+
 def sanitize_name_inputs(inputs_data):
     """
     Sometimes output from Galaxy, or even just file name from user have spaces
@@ -173,7 +165,7 @@
         inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"])
 
 
-def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data, all_datatype_dictionary):
+def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data):
     """
     Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
     and update the dictionary of datatype
@@ -189,9 +181,8 @@
         for key, data_value in inputs_data.items():
             if key == input_false_path:
                 extensionObject = ExtensionClass(input_false_path, data_value)
-
                 datatype_dictionary.update({data_value["order_index"]: extensionObject})
-    all_datatype_dictionary.update(datatype_dictionary)
+    return datatype_dictionary
 
 if __name__ == "__main__":
     main(sys.argv)