diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 24a05a5bc20..0c4d690c519 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -14,27 +14,50 @@ class Registry( object ):
         self.datatypes_by_extension = {}
         self.mimetypes_by_extension = {}
         self.datatype_converters = odict()
+        self.upload_file_formats = []
         self.sniff_order = []
         for ext, kind in datatypes:
+            # Data types are defined in the config like this:
+            # #<file extension> = <data type class>,<mime type (optional)>,<display in upload select list (optional)>
             try:
-                mime_type = None
                 fields = kind.split(",")
-                if len(fields)>1:
-                    kind = fields[0].strip()
-                    mime_type = fields[1].strip()
+                kind = fields[0].strip()
+                mime_type = None
+                display_in_upload = False
+                # See if we have a mime type or a display_in_upload
+                try:
+                    ele = fields[1].strip()
+                    if ele:
+                        if ele == 'display_in_upload':
+                            display_in_upload = True
+                        else:
+                            mime_type = ele
+                except:
+                    pass
+                # See if we have a display_in_upload
+                if not display_in_upload:
+                    try:
+                        ele = fields[2].strip()
+                        if ele == 'display_in_upload':
+                            display_in_upload = True
+                    except:
+                        pass
+                if display_in_upload:
+                    self.upload_file_formats.append( ext )
                 fields = kind.split(":")
                 datatype_module = fields[0]
                 datatype_class = fields[1]
                 fields = datatype_module.split(".")
-                module = __import__(fields.pop(0))
-                for mod in fields: module = getattr(module,mod)
+                module = __import__( fields.pop(0) )
+                for mod in fields:
+                    module = getattr(module,mod)
                 self.datatypes_by_extension[ext] = getattr(module, datatype_class)()
                 if mime_type is None:
                     # Use default mime type as per datatype spec
                     mime_type = self.datatypes_by_extension[ext].get_mime()
                 self.mimetypes_by_extension[ext] = mime_type
-            except:
-                self.log.warning('error loading datatype: %s' % ext)
+            except Exception, e:
+                self.log.warning('error loading datatype "%s", problem: %s' % ( ext, str( e ) ) )
         #default values
         if len(self.datatypes_by_extension) < 1:
             self.datatypes_by_extension = { 
@@ -51,7 +74,7 @@ class Registry( object ):
                 'laj'         : images.Laj(),
                 'lav'         : sequence.Lav(),
                 'maf'         : sequence.Maf(),
-                'qualityscore': qualityscore.QualityScore(),
+                'qual'        : qualityscore.QualityScore(),
                 'scf'         : images.Scf(),
                 'tabular'     : tabular.Tabular(),
                 'taxonomy'    : tabular.Taxonomy(),
@@ -73,7 +96,7 @@ class Registry( object ):
                 'laj'         : 'text/plain',
                 'lav'         : 'text/plain',
                 'maf'         : 'text/plain',
-                'qualityscore': 'text/plain',
+                'qual'        : 'text/plain',
                 'scf'         : 'application/octet-stream',
                 'tabular'     : 'text/plain',
                 'taxonomy'    : 'text/plain',
diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py
index 0c726bc452e..7ec45257d47 100644
--- a/lib/galaxy/tools/parameters/dynamic_options.py
+++ b/lib/galaxy/tools/parameters/dynamic_options.py
@@ -172,8 +172,8 @@ class DynamicOptions( object ):
                 filters[ 'data_meta' ][ 'meta_value' ] = dataset.metadata.species
         except:
             pass
-        return self.generate_options( filters=filters, sep=self.separator )
-    def generate_options( self, filters={}, sep='\t' ):
+        return self.generate_options( trans, filters=filters, sep=self.separator )
+    def generate_options( self, trans, filters={}, sep='\t' ):
         try: 
             meta_key = filters[ 'data_meta' ][ 'meta_key' ]
         except:
@@ -194,7 +194,8 @@ class DynamicOptions( object ):
             return self.generate_for_dbkey( dbkey, meta_key_col, self.name_col, self.value_col, sep=sep )
         else: # meta_key is None
             if self.data_file == 'datatypes_registry':
-                return self.generate_from_datatypes_registry()
+                upload_file_formats = trans.app.datatypes_registry.upload_file_formats
+                return self.generate_from_datatypes_registry( upload_file_formats )
             elif self.data_file == 'encode_datasets.loc':
                 encode_group = filters[ 'params' ][ 'encode_group' ]
                 dbkey = filters[ 'params' ][ 'dbkey' ]
@@ -217,11 +218,9 @@ class DynamicOptions( object ):
                 return self.generate_for_microbial( kingdom, org, feature )
             else:
                 return self.generate( self.name_col, self.value_col, sep=sep )
-    def generate_from_datatypes_registry( self ):
-        from galaxy.datatypes import registry
-        datatypes_registry = registry.Registry()
+    def generate_from_datatypes_registry( self, upload_file_formats ):
         options = []
-        formats = datatypes_registry.datatypes_by_extension.keys()
+        formats = upload_file_formats
         formats.sort()
         options.append( ( 'Auto-detect', 'auto', True ) )
         for format in formats:
diff --git a/test-data/1.fastq b/test-data/1.fastq
new file mode 100644
index 00000000000..abb5f2f25f5
--- /dev/null
+++ b/test-data/1.fastq
@@ -0,0 +1,8 @@
+@seq1  
+GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT  
++seq1  
+hhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh  
+@seq2  
+GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG  
++seq2  
+hhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO
\ No newline at end of file
diff --git a/tools/metag_tools/convert_fastq2fasta.xml b/tools/metag_tools/convert_fastq2fasta.xml
index 0a9185bc886..255d422b5d0 100644
--- a/tools/metag_tools/convert_fastq2fasta.xml
+++ b/tools/metag_tools/convert_fastq2fasta.xml
@@ -1,15 +1,21 @@
 <tool id="convert_fastq2fasta" name="FASTQ-to-FASTA" version="1.0.0">
-    <description>converts FASTQ file to FASTA format</description>
-    <command interpreter="python">convert_fastq2fasta.py $input1 $output1 $output2</command>
-    <inputs>
-        <param name="input1" type="data" format="fastq" label="Fastq file"/>
-    </inputs>
-    <outputs>
-        <data name="output1" format="fasta"/>
-        <data name="output2" format="qualityscore"/>
-    </outputs>
-
-    <help>
+  <description>converts FASTQ file to FASTA format</description>
+  <command interpreter="python">convert_fastq2fasta.py $input1 $output1 $output2</command>
+  <inputs>
+    <param name="input1" type="data" format="fastq" label="Fastq file"/>
+  </inputs>
+  <outputs>
+    <data name="output1" format="qual"/>
+    <data name="output2" format="fasta"/>
+  </outputs>
+  <tests>
+    <!-- NOTE: this tool generates 2 output files, but our functional tests currently only handle the last one generated -->
+    <test>
+      <param name="input1" value="1.fastq" ftype="fastq" />
+      <output name="output2" file="convert_fastq2fasta_out2.fasta" />
+    </test>
+  </tests>
+  <help>
     
 **What it does**
 
diff --git a/tools/metag_tools/rmapq_wrapper.xml b/tools/metag_tools/rmapq_wrapper.xml
index 033af8eff57..0e11c53fc62 100644
--- a/tools/metag_tools/rmapq_wrapper.xml
+++ b/tools/metag_tools/rmapq_wrapper.xml
@@ -10,7 +10,7 @@
             <options from_file="faseq.loc" name_col="0" value_col="1"/>
         </param>
         <param name="input_seq" type="data" format="fasta" label="Sequence file"/>
-        <param name="input_score" type="data" format="qualityscore" label="Quality score file"/>
+        <param name="input_score" type="data" format="qual" label="Quality score file"/>
         <param name="high_score" type="float" size="15" value="40" label="Minimum score for high-quality base (-q)"/>
         <param name="high_len" type="integer" size="15" value="36" label="Minimal high-quality bases (-M)"/>
         <param name="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed"/>
@@ -43,7 +43,7 @@
         <test>
             <param name="database" value="/depot/data2/galaxy/faseq/test" />
             <param name="input_seq" value="rmapq_wrapper_test1.fasta" ftype="fasta"/>
-            <param name="input_score" value="rmapq_wrapper_test1.qualityscore" ftype="qualityscore" />
+            <param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qual" />
             <param name="high_score" value="40" />
             <param name="high_len" value="36" />
             <param name="read_len" value="36" />
diff --git a/tools/metag_tools/short_reads_figure_high_quality_length.xml b/tools/metag_tools/short_reads_figure_high_quality_length.xml
index 407f225dd71..fba61acb112 100644
--- a/tools/metag_tools/short_reads_figure_high_quality_length.xml
+++ b/tools/metag_tools/short_reads_figure_high_quality_length.xml
@@ -5,7 +5,7 @@
 
 <inputs>
 <page>
-    <param name="input1" type="data" format="qualityscore,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
+    <param name="input1" type="data" format="qual,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
     <param name="input2" type="integer" size="5" value="20" label="Quality score threshold" />
 </page>
 </inputs>
@@ -17,12 +17,12 @@
 </requirements>
 <tests>
 	<test>
-		<param name="input1" value="solexa.qualityscore" ftype="qualityscore" />
+		<param name="input1" value="solexa.qual" ftype="qual" />
 		<param name="input2" value="5" />
   		<output name="output1" file="solexa_high_quality_hist.pdf" ftype="pdf"/>
 	</test>
 	<test>
-		<param name="input1" value="454.qualityscore" ftype="qualityscore" />
+		<param name="input1" value="454.qual" ftype="qual" />
 		<param name="input2" value="5" />
 		<output name="output1" file="454_high_quality_hist.pdf" ftype="pdf"/>
 	</test>
diff --git a/tools/metag_tools/short_reads_figure_score.xml b/tools/metag_tools/short_reads_figure_score.xml
index 5181c5156e6..3df38e0cf4d 100644
--- a/tools/metag_tools/short_reads_figure_score.xml
+++ b/tools/metag_tools/short_reads_figure_score.xml
@@ -5,7 +5,7 @@
 
 <inputs>
 <page>
-    <param name="input1" type="data" format="qualityscore, txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
+    <param name="input1" type="data" format="qual, txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
 </page>
 </inputs>
 
@@ -17,11 +17,11 @@
 </requirements>
 <tests>
 	<test>
-		<param name="input1" value="solexa.qualityscore" ftype="qualityscore" />
+		<param name="input1" value="solexa.qual" ftype="qual" />
   		<output name="output1" file="solexaScore.png" ftype="png" />
 	</test>
 	<test>
-		<param name="input1" value="454.qualityscore" ftype="qualityscore" />
+		<param name="input1" value="454.qual" ftype="qual" />
 		<output name="output1" file="454Score.png" ftype="png" />
 	</test>
 </tests>
diff --git a/tools/metag_tools/short_reads_trim_seq.xml b/tools/metag_tools/short_reads_trim_seq.xml
index 8b5bf1a0af7..2af57f6ba39 100644
--- a/tools/metag_tools/short_reads_trim_seq.xml
+++ b/tools/metag_tools/short_reads_trim_seq.xml
@@ -7,7 +7,7 @@
 <inputs>
 <page>
     <param name="input1" type="data" format="fasta,txtseq.zip" label="Reads" />
-    <param name="input2" type="data" format="qualityscore,txtseq.zip" label="Quality scores" />
+    <param name="input2" type="data" format="qual,txtseq.zip" label="Quality scores" />
 	<param name="trim" type="integer" size="5" value="20" label="Minimal quality score" help="bases scoring below this value will trigger splitting"/>
     <param name="length" type="integer" size="5" value="100" label="Minimal length of contiguous segment" help="report all high quality segments above this length. Setting this option to '0' will cause the program to return a single longest run of high quality bases per read" />
     <conditional name="sequencing_method_choice">
@@ -36,7 +36,7 @@
 	<test>
 		<param name="sequencer" value="454" />
 		<param name="input1" value="454.fasta" ftype="fasta" />
-		<param name="input2" value="454.qualityscore" ftype="qualityscore" />
+		<param name="input2" value="454.qual" ftype="qual" />
 		<param name="input3" value="no" />
 		<param name="trim" value="20" />
 		<param name="length" value="0" />
@@ -45,7 +45,7 @@
 	<test>
 		<param name="sequencer" value="Solexa" />
 		<param name="input1" value="solexa.fasta" ftype="fasta" />
-		<param name="input2" value="solexa.qualityscore" ftype="qualityscore" />
+		<param name="input2" value="solexa.qual" ftype="qual" />
 		<param name="input3" value="0" />
 		<param name="trim" value="20" />
 		<param name="length" value="0" />
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index 5c75d2b4560..da60c1ac15b 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -85,7 +85,7 @@ mailing_join_addr = galaxy-user-join@bx.psu.edu
 
 # Mail
 smtp_server = coltrane.bx.psu.edu
-error_email_to = galaxy_bugs@bx.psu.edu
+error_email_to = galaxy-bugs@bx.psu.edu
 
 # Use the new iframe / javascript based layout
 use_new_layout = true
@@ -167,33 +167,34 @@ upload1 = local:///
 
 [galaxy:datatypes]
 
-ab1 = galaxy.datatypes.images:Ab1,application/octet-stream
-axt = galaxy.datatypes.sequence:Axt
-bed = galaxy.datatypes.interval:Bed
-binseq.zip = galaxy.datatypes.images:Binseq,application/zip
+#<file extension> = <data type class>,<mime type (optional)>,<display in upload select list (optional)>
+ab1 = galaxy.datatypes.images:Ab1,application/octet-stream,display_in_upload
+axt = galaxy.datatypes.sequence:Axt,display_in_upload
+bed = galaxy.datatypes.interval:Bed,display_in_upload
+binseq.zip = galaxy.datatypes.images:Binseq,application/zip,display_in_upload
 customtrack = galaxy.datatypes.interval:CustomTrack
 data = galaxy.datatypes.data:Data,application/octet-stream
-fasta = galaxy.datatypes.sequence:Fasta
-fastq = galaxy.datatypes.sequence:Fastq
-gff = galaxy.datatypes.interval:Gff
-gff3 = galaxy.datatypes.interval:Gff3
+fasta = galaxy.datatypes.sequence:Fasta,display_in_upload
+fastq = galaxy.datatypes.sequence:Fastq,display_in_upload
+gff = galaxy.datatypes.interval:Gff,display_in_upload
+gff3 = galaxy.datatypes.interval:Gff3,display_in_upload
 gif = galaxy.datatypes.images:Image,image/gif
 gmaj.zip = galaxy.datatypes.images:Gmaj,application/zip
 html = galaxy.datatypes.images:Html,text/html
-interval = galaxy.datatypes.interval:Interval
+interval = galaxy.datatypes.interval:Interval,display_in_upload
 jpg = galaxy.datatypes.images:Image,image/jpeg
 laj = galaxy.datatypes.images:Laj
 lav = galaxy.datatypes.sequence:Lav
-maf = galaxy.datatypes.sequence:Maf
+maf = galaxy.datatypes.sequence:Maf,display_in_upload
 pdf = galaxy.datatypes.images:Image,application/pdf
 png = galaxy.datatypes.images:Image,image/png
-qualityscore = galaxy.datatypes.qualityscore:QualityScore
-scf = galaxy.datatypes.images:Scf,application/octet-stream
-taxonomy = galaxy.datatypes.tabular:Taxonomy
-tabular = galaxy.datatypes.tabular:Tabular
-txt = galaxy.datatypes.data:Text
-txtseq.zip = galaxy.datatypes.images:Txtseq,application/zip
-wig = galaxy.datatypes.interval:Wiggle
+qual = galaxy.datatypes.qualityscore:QualityScore,display_in_upload
+scf = galaxy.datatypes.images:Scf,application/octet-stream,display_in_upload
+taxonomy = galaxy.datatypes.tabular:Taxonomy,display_in_upload
+tabular = galaxy.datatypes.tabular:Tabular,display_in_upload
+txt = galaxy.datatypes.data:Text,display_in_upload
+txtseq.zip = galaxy.datatypes.images:Txtseq,application/zip,display_in_upload
+wig = galaxy.datatypes.interval:Wiggle,display_in_upload
 #EMBOSS TOOLS
 acedb = galaxy.datatypes.data:Text
 asn1 = galaxy.datatypes.data:Text