--- a/rg_rnaStar.xml	Fri Sep 01 13:17:29 2023 +0000
+++ b/rg_rnaStar.xml	Sun Feb 11 00:01:54 2024 +0000
@@ -91,6 +91,15 @@
         ## Read MAPQ
         --outSAMmapqUnique ${oformat.outSAMmapqUnique}
 
+        ## Transform diploid mode output to reference coordinates
+        #if str($refGenomeSource.geneSource) == 'history':
+            #if 'diploidconditional' in $refGenomeSource:
+                #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
+                    '${refGenomeSource.diploidconditional.genomeTransformOutput}'
+                #end if   
+            #end if
+        #end if
+
         ## Output filter parameters
 
         ## Basic Filters
@@ -318,6 +327,18 @@
                         <expand macro="quantModeNoGTF" />
                     </when>
                 </conditional>
+                <conditional name="diploidconditional">
+                    <param name="diploid" type="select" label="Diploid mode" help="Map RNA-seq reads to a diploid genome">
+                        <option value="No" selected="True">No</option>
+                        <option value="Yes">Yes</option>
+                    </param>
+                    <when value="Yes">
+                        <param argument="--genomeTransformVCF" type="data" format="vcf" label="VCF file with diploid SNVs and InDels" help="The homozygous and heterozygous alleles from this VCF will be inserted into the reference genome to create a transformed genome with two haplotypes"/>
+                        <param argument="--genomeTransformOutput" type="boolean" checked="false" truevalue="--genomeTransformOutput SAM SJ Quant" falsevalue="--genomeTransformOutput None" label="Transform alignments, spliced junctions and quantifications back to                         the reference coordinates" help="Use this if downstream processing relies on reference coordinates"/>
+                    </when>
+                    <when value="No">
+                    </when>
+                </conditional>
             </when>
         </conditional>
 
@@ -810,6 +831,7 @@
 
             <output name="chimeric_junctions" file="test3.chimjunc.tabular" compare="diff" lines_diff="2"/>
         </test>
+        <!-- test 10 -->
         <test expect_num_outputs="3">
             <conditional name="singlePaired">
                 <param name="sPaired" value="single" />
@@ -837,7 +859,7 @@
 
             <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.bam" compare="sim_size" delta="634" />
+            <output name="mapped_reads" file="rnastar_test_mapped_reads_test10.bam" compare="sim_size" delta="634" />
         </test>
         <!-- twopass mode tests -->
         <!-- test Basic twopass -->
@@ -1117,6 +1139,28 @@
             <output name="signal_unique_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" />
             <output name="signal_uniquemultiple_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" />
         </test>
+        <!-- test diploid mode -->
+        <test expect_num_outputs="3">
+            <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.gz" />
+                <param name="genomeSAindexNbases" value="5" />
+            </conditional>
+            <conditional name="diploidconditional">
+                <param name="diploid" value="Yes" />
+                <!-- generated from rnastar_test_mapped_reads.bam with
+                bcftools mpileup and bcftools call -->
+                <param name="genomeTransformVCF" value="rnastar_test_mapped_reads.vcf" ftype="vcf" />
+                <param name="genomeTransformOutput" value="true" />
+            </conditional>
+            <output name="output_log" file="rnastar_test_diploid.log" compare="re_match_multiline" />
+            <output name="splice_junctions" file="rnastar_test_splicejunctions_diploid.bed"/>
+            <output name="mapped_reads" file="rnastar_test_mapped_reads_diploid.bam" compare="sim_size" delta="634" />
+        </test>
       </tests>
     <help><![CDATA[
 **What it does**