--- a/macros.xml	Mon Mar 27 16:37:27 2023 +0000
+++ b/macros.xml	Fri Sep 01 13:17:29 2023 +0000
@@ -5,7 +5,7 @@
     the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
     <!-- STAR version to be used -->
     <token name="@TOOL_VERSION@">2.7.10b</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@VERSION_SUFFIX@">4</token>
     <token name="@PROFILE@">21.01</token>
     <!-- STAR index version compatible with this version of STAR
     This is the STAR version that introduced the index structure expected
@@ -60,6 +60,7 @@
     </xml>
     <xml name="SJDBOPTIONS">
          <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>
+         <param argument="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: 'exon', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as 'gene', 'transcript', 'CDS'."/>
          <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
     </xml>
     <xml name="dbKeyActions">
@@ -103,15 +104,17 @@
                 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
                     --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
                     --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
+                    --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}'
                     #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
                         --sjdbGTFtagExonParentTranscript Parent
                     #end if
                 #end if
             #else:
-                ## ref genome selection is less complex for STARsolo cause
+                ## ref genome selection is less complex for STARsolo because
                 ## with-gtf is mandatory there
                 --sjdbOverhang '${refGenomeSource.sjdbOverhang}'
                 --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}'
+                --sjdbGTFfeatureExon '${refGenomeSource.sjdbGTFfeatureExon}'
                 #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3':
                     --sjdbGTFtagExonParentTranscript Parent
                 #end if
@@ -137,6 +140,7 @@
         #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf':
             --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
             --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
+            --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}'
             #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
                 --sjdbGTFtagExonParentTranscript Parent
             #end if