--- a/macros.xml	Fri Feb 17 20:03:27 2023 +0000
+++ b/macros.xml	Wed Feb 22 18:00:57 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@">0</token>
+    <token name="@VERSION_SUFFIX@">1</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
@@ -64,23 +64,26 @@
     </xml>
     <xml name="dbKeyActions">
         <actions>
-            <conditional name="refGenomeSource.geneSource">
-                <when value="indexed">
-                    <action type="metadata" name="dbkey">
-                        <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
-                            <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                            <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
-                        </option>
-                    </action>
-                </when>
-                <when value="history">
-                    <action type="metadata" name="dbkey">
-                        <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
-                    </action>
-                </when>
-            </conditional>
+            <expand macro="dbKeyAction"/>
         </actions>
     </xml>
+    <xml name="dbKeyAction">
+        <conditional name="refGenomeSource.geneSource">
+            <when value="indexed">
+                <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
+                        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                        <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
+                    </option>
+                </action>
+            </when>
+            <when value="history">
+                <action type="metadata" name="dbkey">
+                    <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
+                </action>
+            </when>
+        </conditional>
+    </xml>
     <token name="@TEMPINDEX@"><![CDATA[
     ## Create temporary index for custom reference
     #if str($refGenomeSource.geneSource) == 'history':
@@ -219,7 +222,7 @@
         </conditional>
     </xml>
     <xml name="umidedup_options">
-        <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other</option>
+        <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other (1MM_All)</option>
         <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option>
         <option value="1MM_Directional" >Directional with stringent UMI deduplication</option>
     </xml>
@@ -231,12 +234,12 @@
     </xml>
     <xml name="cb_match_wl_common">
         <option value="Exact" >Exact</option>
-        <option value="1MM" >Single match</option>
+        <option value="1MM" >Single match (1MM)</option>
     </xml>
     <xml name="cb_match_wl_cellranger">
-        <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option>
-        <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option>
-        <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3)</option>
+        <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2, 1MM_multi)</option>
+        <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3, 1MM_multi_pseudocounts)</option>
+        <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3, 1MM_multi_Nbase_pseudocounts)</option>
     </xml>
     <xml name="solo_adapter_params">
         <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." >
@@ -278,6 +281,7 @@
     <xml name="outCountActions">
         <actions>
             <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
+            <expand macro="dbKeyAction"/>
         </actions>
     </xml>
     <xml name="outWig">
@@ -397,4 +401,13 @@
             <when value="-" />
         </conditional>
     </xml>
+    <xml name="outSAMmapqUnique">
+        <!-- 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." />
+    </xml>
 </macros>

--- 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">