# HG changeset patch
# User iuc
# Date 1552594310 14400
# Node ID 885554d9d1b3207bb030c0bf1d69f4c2e7af2158
# Parent  d397a5703ed8e9795676d988d6ef0cf489efc283
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7

diff -r d397a5703ed8 -r 885554d9d1b3 rg_rnaStar.xml
--- a/rg_rnaStar.xml	Sat Jun 09 14:33:24 2018 -0400
+++ b/rg_rnaStar.xml	Thu Mar 14 16:11:50 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
diff -r d397a5703ed8 -r 885554d9d1b3 test-data/rnastar_test_splicejunctions_twopass.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnastar_test_splicejunctions_twopass.bed	Thu Mar 14 16:11:50 2019 -0400
@@ -0,0 +1,2 @@
+test_chromosome	251	350	1	1	1	30	0	37
+test_chromosome	401	500	1	1	1	26	0	36
diff -r d397a5703ed8 -r 885554d9d1b3 test-data/rnastar_test_twopass.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnastar_test_twopass.log	Thu Mar 14 16:11:50 2019 -0400
@@ -0,0 +1,34 @@
+                                 Started job on |	Feb 12 11:19:46
+                             Started mapping on |	Feb 12 11:20:03
+                                    Finished on |	Feb 12 11:20:03
+       Mapping speed, Million of reads per hour |	inf
+
+                          Number of input reads |	100
+                      Average input read length |	75
+                                    UNIQUE READS:
+                   Uniquely mapped reads number |	99
+                        Uniquely mapped reads % |	99.00%
+                          Average mapped length |	74.84
+                       Number of splices: Total |	56
+            Number of splices: Annotated (sjdb) |	56
+                       Number of splices: GT/AG |	56
+                       Number of splices: GC/AG |	0
+                       Number of splices: AT/AC |	0
+               Number of splices: Non-canonical |	0
+                      Mismatch rate per base, % |	2.01%
+                         Deletion rate per base |	0.00%
+                        Deletion average length |	0.00
+                        Insertion rate per base |	0.00%
+                       Insertion average length |	0.00
+                             MULTI-MAPPING READS:
+        Number of reads mapped to multiple loci |	1
+             % of reads mapped to multiple loci |	1.00%
+        Number of reads mapped to too many loci |	0
+             % of reads mapped to too many loci |	0.00%
+                                  UNMAPPED READS:
+       % of reads unmapped: too many mismatches |	0.00%
+                 % of reads unmapped: too short |	0.00%
+                     % of reads unmapped: other |	0.00%
+                                  CHIMERIC READS:
+                       Number of chimeric reads |	0
+                            % of chimeric reads |	0.00%