--- a/ensembl_variant_report.xml	Fri Jan 06 17:43:29 2017 -0500
+++ b/ensembl_variant_report.xml	Mon Feb 06 09:25:43 2017 -0500
@@ -20,12 +20,12 @@
              --format=snpeff
          #else
              --input="$variant.input_tsv"
-            --pos_column=$pos_column
-            --ref_column=$ref_column
-            --alt_column=$alt_column
-            --transcript_column=$transcript_column
-            --dp_column=$dp_column
-            --dpr_column=$dpr_column
+            --pos_column=$variant.pos_column
+            --ref_column=$variant.ref_column
+            --alt_column=$variant.alt_column
+            --transcript_column=$variant.transcript_column
+            --dp_column=$variant.dp_column
+            --dpr_column=$variant.dpr_column
          #end if
          #if str($filter.min_depth) != '':
              --min_depth=$filter.min_depth
@@ -46,7 +46,7 @@
     ]]></command>
     <inputs>
         <conditional name="variant">
-            <param name="fmt" type="select" label="">
+            <param name="fmt" type="select" label="Input format for variants">
                 <option value="vcf">snpEff vcf</option>
                 <option value="tsv">tabular from snpsift extract</option>
             </param>
@@ -54,7 +54,7 @@
                 <param name="input_vcf" type="data" format="vcf" label="snpEff VCF file"/>
             </when>
             <when value="tsv">
-                <param name="input_tsv" type="data" format="vcf" label="tabular file"/>
+                <param name="input_tsv" type="data" format="tabular" label="tabular file"/>
                 <param name="pos_column" type="data_column" data_ref="input_tsv" label="POS column"/>
                 <param name="ref_column" type="data_column" data_ref="input_tsv" label="REF column"/>
                 <param name="alt_column" type="data_column" data_ref="input_tsv" label="ALT column"/>
@@ -69,7 +69,7 @@
                 <option value="history">History</option>
             </param>
             <when value="cached">
-                <param name="ref_loc" type="data" format="twobit" label="Select reference 2bit file">
+                <param name="ref_loc" type="select" label="Select reference 2bit file">
                     <options from_data_table="twobit" />
                 </param>
             </when>