--- a/rg_rnaStar.xml	Sat Jun 09 14:33:39 2018 -0400
+++ b/rg_rnaStar.xml	Thu Mar 14 16:12:38 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="rna_star" name="RNA STAR" version="2.6.0b-1" profile="17.01">
+<tool id="rna_star" name="RNA STAR" version="2.6.0b-2" profile="17.01">
     <description>Gapped-read mapper for RNA-seq data</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    
+
     <stdio>
         <regex match="FATAL error" source="both" level="fatal"/>
         <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
@@ -143,7 +143,7 @@
             --seedPerReadNmax "$params.seed.seedPerReadNmax"
             --seedPerWindowNmax "$params.seed.seedPerWindowNmax"
             --seedNoneLociPerWindow "$params.seed.seedNoneLociPerWindow"
-        
+
             ## Alignment parameter options
             --alignIntronMin "$params.align.alignIntronMin"
             --alignIntronMax "$params.align.alignIntronMax"
@@ -161,6 +161,9 @@
             --twopassMode "$params.twopass.twopassMode"
             #if str( $params.twopass.twopassMode ) == "Basic":
                 --twopass1readsN "$params.twopass.twopass1readsN"
+                #if not $refGenomeSource.sjdbGTFfile:
+                    --sjdbOverhang '$refGenomeSource.sjdbOverhang'
+                #end if
             #end if
 
             ## Chimeric alignment parameter options
@@ -241,7 +244,7 @@
                                 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                             </options>
                         </param>
-                        
+
                         <expand macro="@SJDBOPTIONS@" />
                     </when>
                 </conditional>
@@ -278,7 +281,7 @@
                     <option value="RemoveInconsistentStrands" selected="true">Remove alignments that have junctions with inconsistent strands</option>
                     <option value="None">No filtering</option>
                 </param>
-  
+
               <!-- Additional output parameter settings. -->
               <conditional name="output_params2">
                   <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?">
@@ -321,7 +324,7 @@
             </param>
             <when value="default"/>
             <when value="star_fusion"/><!-- Set STAR-fusion parameters automatically -->
-  
+
             <when value="full">
                 <section name="seed" title="Seed parameters" expanded="False">
                     <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
@@ -332,7 +335,7 @@
                     <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
                     <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
                 </section>
-    
+
                 <section name="align" title="Alignment parameters" expanded="False">
                     <param argument="--alignIntronMin" name="alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
                     <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
@@ -358,7 +361,7 @@
                     <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">
                     <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
                         <option value="no" selected="true">No</option>
@@ -404,7 +407,7 @@
         <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
             <expand macro="dbKeyActions" />
         </data>
-        
+
         <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
             <filter>quantMode is True</filter>
             <expand macro="dbKeyActions" />
@@ -422,7 +425,7 @@
             <param name="outSAMattributes" value="All" />
             <param name="outSAMstrandField" value="intronMotif" />
             <param name="settingsType" value="default" />
-            
+
             <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
             <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
             <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
@@ -441,7 +444,7 @@
             <param name="outSAMattributes" value="All" />
             <param name="outSAMstrandField" value="intronMotif" />
             <param name="settingsType" value="default" />
-            
+
             <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
             <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
             <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
@@ -452,12 +455,12 @@
             <param name="geneSource" value="history" />
             <param name="genomeFastaFiles" value="tophat_test.fa" />
             <param name="sPaired" value="single" />
-            
+
             <param name="output_select" value="yes" />
             <param name="outSAMattributes" value="All" />
             <param name="outSAMstrandField" value="intronMotif" />
             <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
-            
+
             <param name="output_select2" value="yes" />
             <param name="outFilterScoreMinOverLread" value="0.9" />
             <param name="settingsType" value="full" />
@@ -508,11 +511,32 @@
             <param name="output_select2" value="yes" />
             <param name="settingsType" value="full" />
             <param name="chim_select" value="false" />
-            
+
             <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
             <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
             <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
         </test>
+        <test>
+            <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
+            <param name="geneSource" value="history" />
+            <param name="genomeFastaFiles" value="tophat_test.fa" />
+            <param name="sPaired" value="single" />
+
+            <param name="output_select" value="yes" />
+            <param name="outSAMattributes" value="All" />
+            <param name="outSAMstrandField" value="intronMotif" />
+            <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
+
+            <param name="output_select2" value="yes" />
+            <param name="settingsType" value="full" />
+            <param name="twopass" value="true" />
+            <param name="twopassMode" value="Basic" />
+            <param name="chim_select" value="false" />
+
+            <output name="output_log" file="rnastar_test_twopass.log" compare="diff" lines_diff="12"/>
+            <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
+            <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
+        </test>
     </tests>
     <help>
 **What it does**
@@ -550,13 +574,12 @@
 
 Galaxy_ (that's what you are using right now!) for gluing everything together
 
-Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper
+Most of the work for this wrapper XML is Jeremy Goecks' original STAR wrapper
 
 Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies
 and odds and ends of other code and documentation comprising this tool was
 written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts
 
-.. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs