--- a/extract_genomic_dna.xml	Thu Jan 14 07:55:22 2016 -0500
+++ b/extract_genomic_dna.xml	Thu Jan 14 09:24:51 2016 -0500
@@ -1,18 +1,20 @@
 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.0">
     <description>using coordinates from assembled/unassembled genomes</description>
+    <requirements>
+        <requirement type="package" version="35x1">faToTwoBit</requirement>
+    </requirements>
     <command>
         <![CDATA[
-            #set input_format $input_format_cond.input_format
-            #set input $input_format_cond.input
-            #set dbkey = $input.metadata.dbkey
+            #set input_format $input.ext
+            #set genome = $input.metadata.dbkey
             #set datatype = $input.datatype
             mkdir -p output_dir &&
             python $__tool_directory__/extract_genomic_dna.py
             --input_format $input_format
             --input "$input"
-            --dbkey $dbkey
+            --genome "$genome"
             #if str($input_format) == "gff":
-                --interpret_features $input_format_cond.interpret_features
+                --interpret_features $interpret_features
             #end if
             #if isinstance($datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
                 --columns "1,4,5,7"
@@ -30,26 +32,13 @@
         ]]>
     </command>
     <inputs>
-        <conditional name="input_format_cond">
-            <param name="input_format" type="select" label="Input file format">
-                <option value="gff" selected="True">Gff</option>
-                <option value="interval">Interval</option>
-            </param>
-            <when value="gff">
-                <param name="input" type="data" format="gff" label="Fetch sequences for intervals in">
-                    <validator type="unspecified_build" />
-                </param>
-                <param name="interpret_features" type="select" label="Interpret features when possible">
-                    <option value="yes">Yes</option>
-                    <option value="no">No</option>
-                </param>
-            </when>
-            <when value="interval">
-                <param name="input" type="data" format="interval" label="Fetch sequences for intervals in">
-                    <validator type="unspecified_build" />
-                </param>
-            </when>
-        </conditional>
+        <param name="input" type="data" format="gff,interval" label="Fetch sequences for intervals in" help="Supported formats are gff, interval">
+            <validator type="unspecified_build" />
+        </param>
+        <param name="interpret_features" type="select" label="Interpret features when possible" help="Applicable only when input dataset format is gff">
+            <option value="yes">Yes</option>
+            <option value="no">No</option>
+        </param>
         <conditional name="reference_genome_cond">
             <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
                 <option value="cached">locally cached</option>
@@ -57,8 +46,8 @@
             </param>
             <when value="cached">
                 <param name="reference_genome" type="select" label="Using reference genome">
-                    <options from_data_table="alignseq_seq">
-                        <filter type="data_meta" key="dbkey" ref="input" column="dbkey"/>
+                    <options from_data_table="twobit">
+                        <filter type="data_meta" key="dbkey" ref="input" column="0"/>
                     </options>
                     <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                 </param>
@@ -66,7 +55,7 @@
             <when value="history">
                 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
                     <options>
-                        <filter type="data_meta" key="dbkey" ref="input_bam" />
+                        <filter type="data_meta" key="dbkey" ref="input"/>
                     </options>
                     <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
                 </param>