--- a/picard_CollectRnaSeqMetrics.xml	Mon Feb 17 10:24:29 2020 -0500
+++ b/picard_CollectRnaSeqMetrics.xml	Wed Feb 19 14:27:00 2020 -0500
@@ -2,7 +2,7 @@
     <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description>
     <macros>
         <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@WRAPPER_VERSION@">2</token>
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="3.4.1">r-base</requirement>
@@ -22,18 +22,16 @@
       ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format
 
       #if str($gene_reference_source.gene_reference_source_selector) == "gtf"
-        #if $gene_reference_source.refFlat.ext != 'gff3'
-            gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw &&
+        #if $gene_reference_source.refFlat.ext == 'gff3'
+            gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
         #else
-            gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
+            gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw &&
         #end if
-
         grep -v '^#' refFlat.tab.raw | awk '{print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &&
       #else
-        grep -v '^#' ${refFlat} | awk '{print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &&
+        grep -v '^#' ${refFlat} | awk '{if ($3 == "+" || $3 == "-") print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10; else print}' > refFlat.tab &&
       #end if
 
-
       ## Start picard command
 
       @java_options@
@@ -145,6 +143,20 @@
       <param name="rrna_fragment_percentage" value="0.8" />
       <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
     </test>
+   <test>
+      <param name="reference_source_selector" value="history"/>
+      <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
+      <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
+      <param name="assume_sorted" value="true" />
+
+      <param name="gene_reference_source_selector" value="refflat" />
+      <param name="refFlat" value="picard_CollectRnaSeqMetrics.ucsc_output" />
+      <param name="metric_accumulation_level" value="ALL_READS" />
+      <param name="minimum_length" value="500" />
+      <param name="strand_specificity" value="NONE" />
+      <param name="rrna_fragment_percentage" value="0.8" />
+      <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
+    </test>
 
     <test>
       <param name="reference_source_selector" value="history"/>