--- a/rg_rnaStar.xml	Mon Mar 27 16:37:27 2023 +0000
+++ b/rg_rnaStar.xml	Fri Sep 01 13:17:29 2023 +0000
@@ -628,6 +628,44 @@
                 <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
             </output>
         </test>
+        <!-- Test if an alternative feature can be provided as a splicing unit.
+         If the splice feature set is not set correctly,
+        "Fatal INPUT FILE error, no exon lines in the GTF file" is expected -->
+        <test expect_num_outputs="4">
+            <conditional name="singlePaired">
+                <param name="sPaired" value="single" />
+                <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
+            </conditional>
+            <conditional name="refGenomeSource">
+                <param name="geneSource" value="history" />
+                <param name="genomeFastaFiles" value="tophat_test.fa" />
+                <param name="genomeSAindexNbases" value="5" />
+                <conditional name="GTFconditional">
+                    <param name="GTFselect" value="with-gtf" />
+                    <param name="sjdbOverhang" value="75"/>
+                    <param name="sjdbGTFfile" value="no_exon.gtf" ftype="gtf"/>
+                    <param name="sjdbGTFfeatureExon" value="fakexon"/>
+                    <conditional name="quantmode_output">
+                        <param name="quantMode" value="GeneCounts"/>
+                    </conditional>
+                </conditional>
+            </conditional>
+            <section name="oformat">
+                <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
+            </section>
+            <section name="algo">
+                <conditional name="params">
+                    <param name="settingsType" value="default" />
+                </conditional>
+            </section>
+
+            <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
+            <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
+            <output name="mapped_reads" file="rnastar_test_mapped_reads_fakexon.bam" compare="sim_size" delta="634" />
+            <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt">
+                <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
+            </output>
+        </test>
         <!-- test gtf file and TranscriptomeSAM mode -->
         <test expect_num_outputs="4">
             <conditional name="singlePaired">