--- a/rg_rnaStar.xml	Fri Feb 17 20:03:27 2023 +0000
+++ b/rg_rnaStar.xml	Wed Feb 22 18:00:57 2023 +0000
@@ -386,13 +386,7 @@
             label="Would you like all alignments with the best score labeled
             primary?"/> -->
             <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" />
-            <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value
-            - according to SAM/BAM specs it means "undefined".
-            - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. -->
-            <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255"
-            label="MAPQ value for unique mappers"
-            help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is
-used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." />
+            <expand macro="outSAMmapqUnique"/>
         </section>
         <section name="filter" title="Output filter criteria" expanded="true">
             <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true"
@@ -419,7 +413,7 @@
                     <param argument="--outFilterScoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output"/>
                     <param argument="--outFilterMatchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output"/>
                     <param argument="--outFilterMatchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output"/>
-                    <param argument="--outSAMmultNmax" type="integer" value="-1" min="-1" label="Maximum number of multimapping alignments to output for a read" help="A value of -1 (the default) results in all alignments (up to –-outFilterMultimapNmax) being output" />
+                    <param argument="--outSAMmultNmax" type="integer" value="-1" min="-1" label="Maximum number of multimapping alignments to output for a read" help="A value of -1 (the default) results in all alignments (up to --outFilterMultimapNmax) being output" />
                     <param argument="--outSAMtlen" type="select" label="Calculation method for TLEN">
                         <option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option>
                         <option value="2">leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends</option>
@@ -546,7 +540,6 @@
 
         <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
             <filter>'GeneCounts' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter>
-            <expand macro="dbKeyActions" />
             <expand macro="outCountActions" />
         </data>
         <expand macro="outWigOutputs"/>
@@ -631,7 +624,9 @@
             <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="reads_per_gene" file="tophat_test_reads_per_gene.txt" />
+            <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">