--- a/extract_genomic_dna.xml	Thu Jan 14 10:43:42 2016 -0500
+++ b/extract_genomic_dna.xml	Thu Jan 14 10:51:45 2016 -0500
@@ -5,20 +5,18 @@
     </requirements>
     <command>
         <![CDATA[
-            #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"
             --genome "$genome"
-            #if str($input_format) == "gff":
+            #if isinstance($datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
+                --input_format "gff"
+                --columns "1,4,5,7"
                 --interpret_features $interpret_features
-            #end if
-            #if isinstance($datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
-                --columns "1,4,5,7"
             #else:
+                --input_format "interval"
                 --columns "${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}"
             #end if
             --reference_genome_source $reference_genome_cond.reference_genome_source
@@ -79,7 +77,7 @@
             <param name="interpret_features" value="yes"/>
             <param name="index_source" value="cached"/>
             <param name="out_format" value="fasta"/>
-            <output name="out_file1">
+            <output name="out_file1" file="extract_genomic_dna_out1.fasta">
                 <assert_contents>
                     <!-- First few lines... -->
                     <has_text text=">hg17_chr1_147962192_147962580_- CCDS989.1_cds_0_0_chr1_147962193_r" />
@@ -100,7 +98,7 @@
             <param name="interpret_features" value="yes"/>
             <param name="index_source" value="cached"/>
             <param name="out_format" value="fasta"/>
-            <output name="out_file1" file="extract_genomic_dna_out2.fasta" />
+            <output name="out_file1" file="extract_genomic_dna_out2.fasta" compare="contains"/>
         </test>
         <test>
             <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
@@ -115,14 +113,14 @@
             <param name="interpret_features" value="no"/>
             <param name="index_source" value="cached"/>
             <param name="out_format" value="interval"/>
-            <output name="out_file1" file="extract_genomic_dna_out4.gff" />
+            <output name="out_file1" file="extract_genomic_dna_out4.gff" compare="contains"/>
         </test>
         <test>
             <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="no"/>
             <param name="out_format" value="fasta"/>
             <param name="index_source" value="cached"/>
-            <output name="out_file1" file="extract_genomic_dna_out5.fasta" />
+            <output name="out_file1" file="extract_genomic_dna_out5.fasta" compare="contains"/>
         </test>
         <!-- Test custom sequences support and GFF feature interpretation. -->
         <test>
@@ -131,7 +129,7 @@
             <param name="index_source" value="history"/>
             <param name="ref_file" value="tophat_in1.fasta"/>
             <param name="out_format" value="fasta"/>
-            <output name="out_file1" file="extract_genomic_dna_out6.fasta" />
+            <output name="out_file1" file="extract_genomic_dna_out6.fasta" compare="contains"/>
         </test>
         <test>
             <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
@@ -139,7 +137,7 @@
             <param name="index_source" value="history"/>
             <param name="ref_file" value="tophat_in1.fasta"/>
             <param name="out_format" value="fasta"/>
-            <output name="out_file1" file="extract_genomic_dna_out7.fasta" />
+            <output name="out_file1" file="extract_genomic_dna_out7.fasta" compare="contains"/>
         </test>
     </tests>
     <help>