# HG changeset patch
# User iuc
# Date 1519923388 18000
# Node ID 2055c2667eb34571f926ae86da6d21c124a1fe63
# Parent  99b17b74a8cdcea0f21b02a25df28921ce5fa9b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 427913231c5894bde2b2ed428da2b8aee30bc311

diff -r 99b17b74a8cd -r 2055c2667eb3 rg_rnaStar.xml
--- a/rg_rnaStar.xml	Thu Oct 12 04:59:08 2017 -0400
+++ b/rg_rnaStar.xml	Thu Mar 01 11:56:28 2018 -0500
@@ -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>
@@ -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 +151,12 @@
             --alignTranscriptsPerReadNmax "$params.align.alignTranscriptsPerReadNmax"
             --alignEndsType $params.align.alignEndsType
 
+            ## Two pass mode
+            --twopassMode "$params.twopass.twopassMode"
+            #if str( $params.twopass.twopassMode ) == "Basic":
+                --twopass1readsN "$params.twopass.twopass1readsN"
+            #end if
+
             ## Chimeric alignment parameter options
             #if str( $params.chim.chim_select ) == "yes":
                 --chimSegmentMin "$params.chim.chimSegmentMin"
@@ -325,11 +332,16 @@
                     <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 +583,6 @@
 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