From 9016aa63cb7064b60fac33776f8b8f9cf9a17498 Mon Sep 17 00:00:00 2001
From: Torsten Houwaart <houwaart@informatik.uni-freiburg.de>
Date: Fri, 16 Feb 2018 17:14:14 +0100
Subject: [PATCH 1/5] Add two pass mode

---
 tools/rgrnastar/rg_rnaStar.xml | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/tools/rgrnastar/rg_rnaStar.xml b/tools/rgrnastar/rg_rnaStar.xml
index 476a1544baa..42f649dafbc 100644
--- a/tools/rgrnastar/rg_rnaStar.xml
+++ b/tools/rgrnastar/rg_rnaStar.xml
@@ -120,8 +120,9 @@
             --alignSJDBoverhangMin 10
             --alignMatesGapMax 200000
             --alignIntronMax 200000
+            --twopassMode Basic
+            --twopass1readsN -1
 
-            ## --twopass1readsN 100000000  
             ## --chimSegmentReadGapMax 3              ## not an option in STAR 2.4.0
             ## --alignSJstitchMismatchNmax 5 -1 5 5   ## not an option in STAR 2.4.0
 
@@ -150,6 +151,10 @@
             --alignTranscriptsPerReadNmax "$params.align.alignTranscriptsPerReadNmax"
             --alignEndsType $params.align.alignEndsType
 
+            ## Two pass mode
+            --twopassMode "$params.twopass.twopassMode"
+            --twopass1readsN "$params.twopass.twopass1readsN"
+
             ## Chimeric alignment parameter options
             #if str( $params.chim.chim_select ) == "yes":
                 --chimSegmentMin "$params.chim.chimSegmentMin"
@@ -325,11 +330,16 @@
                     <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/>
                 </section>
 
+                <section name="twopass" title="Two pass mode" expanded="False">
+                    <param argument="--twopassMode" type="boolean" truevalue="Basic" falsevalue="None" checked="false" label="Use two pass mode to better map reads to unknown splice junctions"/>
+                    <param argument="--twopass1readsN" type="integer" min="-1" value="-1" label="Number of reads to map in the first pass (-1: all)"/>
+                </section>
+
                 <section name="limits" title="Limits" expanded="False">
                     <param argument="--limitBAMsortRAM" type="integer" min="0" value="0" label="Maximum available RAM (in bytes) for sorting" help="If 0, this will be set to the genome index size. This is typically only changed in cases where an error is produced." />
-	            <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
-	            <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
-	            <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
+	                <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
+	                <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
+	                <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
                 </section>
     
                 <conditional name="chim">
@@ -571,7 +581,6 @@ The All option includes the Standard attributes, plus the following four::
 STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running
 STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::
 
-  --twopassMode Basic                   # not an option in STAR 2.4.0
   --chimSegmentReadGapMax 3             # not an option in STAR 2.4.0
   --alignSJstitchMismatchNmax 5 -1 5 5  # not an option in STAR 2.4.0
 

From 26e4eacb268f897fa54cc2d12058cd2bf6ec94a4 Mon Sep 17 00:00:00 2001
From: Torsten Houwaart <houwaart@informatik.uni-freiburg.de>
Date: Fri, 16 Feb 2018 17:20:23 +0100
Subject: [PATCH 2/5] Fix whitespace.

---
 tools/rgrnastar/rg_rnaStar.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/rgrnastar/rg_rnaStar.xml b/tools/rgrnastar/rg_rnaStar.xml
index 42f649dafbc..c1ee4c8e7ef 100644
--- a/tools/rgrnastar/rg_rnaStar.xml
+++ b/tools/rgrnastar/rg_rnaStar.xml
@@ -337,9 +337,9 @@
 
                 <section name="limits" title="Limits" expanded="False">
                     <param argument="--limitBAMsortRAM" type="integer" min="0" value="0" label="Maximum available RAM (in bytes) for sorting" help="If 0, this will be set to the genome index size. This is typically only changed in cases where an error is produced." />
-	                <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
-	                <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
-	                <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
+                    <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
+                    <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
+                    <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
                 </section>
     
                 <conditional name="chim">

From 8895f54204f2f1575f01ca99dfcb16535384fa14 Mon Sep 17 00:00:00 2001
From: Torsten Houwaart <houwaart@informatik.uni-freiburg.de>
Date: Fri, 16 Feb 2018 17:47:59 +0100
Subject: [PATCH 3/5] Avoid parameter conflict

---
 tools/rgrnastar/rg_rnaStar.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/rgrnastar/rg_rnaStar.xml b/tools/rgrnastar/rg_rnaStar.xml
index c1ee4c8e7ef..eb08b5adc1c 100644
--- a/tools/rgrnastar/rg_rnaStar.xml
+++ b/tools/rgrnastar/rg_rnaStar.xml
@@ -153,7 +153,8 @@
 
             ## Two pass mode
             --twopassMode "$params.twopass.twopassMode"
-            --twopass1readsN "$params.twopass.twopass1readsN"
+            # if str( $params.twopass.twopassMode ) == "Basic":
+                --twopass1readsN "$params.twopass.twopass1readsN"
 
             ## Chimeric alignment parameter options
             #if str( $params.chim.chim_select ) == "yes":

From b47c1a275137ba3ac7c16b2d1875bda8bddac801 Mon Sep 17 00:00:00 2001
From: Torsten Houwaart <houwaart@informatik.uni-freiburg.de>
Date: Fri, 16 Feb 2018 17:49:02 +0100
Subject: [PATCH 4/5] Closing if

---
 tools/rgrnastar/rg_rnaStar.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/rgrnastar/rg_rnaStar.xml b/tools/rgrnastar/rg_rnaStar.xml
index eb08b5adc1c..95f115a9014 100644
--- a/tools/rgrnastar/rg_rnaStar.xml
+++ b/tools/rgrnastar/rg_rnaStar.xml
@@ -153,8 +153,9 @@
 
             ## Two pass mode
             --twopassMode "$params.twopass.twopassMode"
-            # if str( $params.twopass.twopassMode ) == "Basic":
+            #if str( $params.twopass.twopassMode ) == "Basic":
                 --twopass1readsN "$params.twopass.twopass1readsN"
+            #end if
 
             ## Chimeric alignment parameter options
             #if str( $params.chim.chim_select ) == "yes":

From e4267f8db9b8476f888033957ad3a2bf572f2aea Mon Sep 17 00:00:00 2001
From: Torsten Houwaart <houwaart@informatik.uni-freiburg.de>
Date: Fri, 16 Feb 2018 20:20:50 +0100
Subject: [PATCH 5/5] Bump version

---
 tools/rgrnastar/rg_rnaStar.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/rgrnastar/rg_rnaStar.xml b/tools/rgrnastar/rg_rnaStar.xml
index 95f115a9014..11ef0855dcd 100644
--- a/tools/rgrnastar/rg_rnaStar.xml
+++ b/tools/rgrnastar/rg_rnaStar.xml
@@ -1,4 +1,4 @@
-<tool id="rna_star" name="RNA STAR" version="2.5.2b-1" profile="17.01">
+<tool id="rna_star" name="RNA STAR" version="2.5.2b-2" profile="17.01">
     <description>Gapped-read mapper for RNA-seq data</description>
     <macros>
         <import>macros.xml</import>