Add WASP mode to STAR as requested by a user

tools/rgrnastar/rg_rnaStar.xml

@@ -47,9 +47,11 @@
 
         ## Two pass mode
         --twopassMode ${twopass.twopassMode} ${twopass.twopass_read_subset}
-        #for $sj_input in $twopass.sj_precalculated:
-            '$sj_input'
-        #end for
+        #if str($twopass.sj_precalculated).strip():
+            #for $sj_input in $twopass.sj_precalculated:
+                '$sj_input'
+            #end for
+        #end if
         #if str($twopass.twopassMode) != 'None':
             #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
                 ## need to check first if its a cached index or from history
@@ -215,7 +217,7 @@
             #end if
 
             ## Limits
-                @LIMITS@
+            @LIMITS@
         #else:
             ## Go with STAR's default algorithmic settings,
             ## but we need to provide a reasonable default
@@ -232,12 +234,16 @@
                 #end if
             #end if
         #end if
-
         --outBAMsortingThreadN \${GALAXY_SLOTS:-4}
         --outBAMsortingBinsN $perf.outBAMsortingBinsN
         --winAnchorMultimapNmax $perf.winAnchorMultimapNmax
         --limitBAMsortRAM \$((\${GALAXY_MEMORY_MB:-0}*1000000))
 
+        #if $oformat.wasp_conditional.waspOutputMode == "wasp_mode":
+            --waspOutputMode SAMtag
+            --varVCFfile '$oformat.wasp_conditional.varVCFfile'
+        #end if
+
         ## Handle chimeric options and output
         #if str($chimOutType):
             --chimOutType $chimOutType
@@ -408,6 +414,7 @@ with Cufflinks if your sequences come from an unstranded library preparation.">
             primary?"/> -->
             <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" />
             <expand macro="outSAMmapqUnique"/>
+            <expand macro="wasp"/>
         </section>
         <section name="filter" title="Output filter criteria" expanded="true">
             <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true"
@@ -565,29 +572,32 @@ with Cufflinks if your sequences come from an unstranded library preparation.">
         </data>
         <expand macro="outWigOutputs"/>
     </outputs>
-
     <tests>
         <test expect_num_outputs="3">
             <conditional name="singlePaired">
-                <param name="sPaired" value="single" />
-                <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
+                <param name="sPaired" value="paired" />
+                <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
+                <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
             </conditional>
             <conditional name="refGenomeSource">
                 <param name="geneSource" value="history" />
-                <param name="genomeFastaFiles" value="tophat_test.fa.gz" />
+                <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
                 <param name="genomeSAindexNbases" value="5" />
             </conditional>
             <section name="oformat">
                 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
+                <conditional name="wasp_conditional">
+                    <param name="waspOutputMode" value="wasp_mode"/>
+                    <param name="varVCFfile" value="filtered3.vcf" ftype="vcf" />
+                </conditional>
             </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.bam" compare="sim_size" delta="634" />
+            <output name="splice_junctions" file="rnastar_test_splicejunctions_wasp.bed"/>
         </test>
         <!-- test with cached genome index -->
         <test expect_num_outputs="3">

tools/rgrnastar/rg_rnaStarSolo.xml

@@ -94,6 +94,11 @@
     --soloCBwhitelist None
     #end if
 
+    #if $solo.wasp_conditional.waspOutputMode == "wasp_mode":
+        --waspOutputMode SAMtag
+        --varVCFfile '$solo.wasp_conditional.varVCFfile'
+    #end if
+
     --soloStrand $solo.soloStrand
     --soloFeatures $solo.soloFeatures
     --soloUMIdedup $sc.umidedup.soloUMIdedup
@@ -355,6 +360,7 @@
                 <option value="GeneFull_Ex50pAS" >Full: Count all reads overlapping genes' exons and introns: prioritize 50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction.</option>
                 <option value="Gene Velocyto">Velocyto: calculate spliced, unspliced, and ambiguous counts per cell per gene similar to the velocyto tool</option>
             </param>
+            <expand macro="wasp"/>
             <conditional name="filter" >
                 <param name="filter_type" type="select" label="Cell filtering type and parameters" >
                     <option value="cellranger2" selected="true" >Simple filtering of CellRanger v2</option>
@@ -515,6 +521,10 @@
                 <param name="soloStrand" value="Forward" />
                 <param name="soloFeatures" value="Gene" />
                 <param name="quantModeGene" value="true" />
+                <conditional name="wasp_conditional">
+                    <param name="waspOutputMode" value="wasp_mode"/>
+                    <param name="varVCFfile" value="filtered3.vcf" ftype="vcf" />
+                </conditional>
             </section>
             <output name="output_barcodes" >
                 <assert_contents>
@@ -544,7 +554,7 @@
                     <has_line_matching expression="\s+yesUMIs\s+8" />
                 </assert_contents>
             </output>
-            <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />
+            <output name="output_BAM" value="filtered4.bam" ftype="bam" lines_diff="6"/>
             <output name="reads_per_gene" >
                 <assert_contents>
                     <has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" />