diff --git a/tools/rgrnastar/macros.xml b/tools/rgrnastar/macros.xml
index c67a80da9a0..d5ab47d0099 100644
--- a/tools/rgrnastar/macros.xml
+++ b/tools/rgrnastar/macros.xml
@@ -5,7 +5,7 @@
the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
2.7.11a
- 0
+ 1
21.01
-
+
@@ -352,73 +344,92 @@
outWig['outWigType'] != "None"
-
+
-
+
outWig['outWigType'] != "None"
-
+
-
+
outWig['outWigType'] != "None" and outWig['outWigStrand']
-
+
-
+
outWig['outWigType'] != "None" and outWig['outWigStrand']
-
+
-
+
-
+
-
-
+
+
-
+
-
+
-
+
-
+
-
+
+
+
+
+
+
+
+ - vW:i:2 = multi-mapping read
+ - vW:i:3 = variant base in the read is N (non-ACGT)
+ - vW:i:4 = remapped read did not map
+ - vW:i:5 = remapped read multi-maps
+ - vW:i:6 = remapped read maps to a different locus
+ - vW:i:7 = read overlaps too many variants
+ ]]>
+
+
+
+
+
+
+
+
+
diff --git a/tools/rgrnastar/rg_rnaStar.xml b/tools/rgrnastar/rg_rnaStar.xml
index 6becaac2dfe..45998e2e08f 100644
--- a/tools/rgrnastar/rg_rnaStar.xml
+++ b/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?"/> -->
+
-
-
-
+
+
+
-
+
@@ -586,8 +597,7 @@ with Cufflinks if your sequences come from an unstranded library preparation.">
-
-
+
diff --git a/tools/rgrnastar/rg_rnaStarSolo.xml b/tools/rgrnastar/rg_rnaStarSolo.xml
index dee71c1b7dd..8835b5feae4 100644
--- a/tools/rgrnastar/rg_rnaStarSolo.xml
+++ b/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 @@
+
@@ -515,6 +521,10 @@
+
+
+
+
-
+