# HG changeset patch
# User iuc
# Date 1526506263 14400
# Node ID a70a7eebb4350d87cbbfdf9b10c977de16daf677
# Parent  2055c2667eb34571f926ae86da6d21c124a1fe63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c

diff -r 2055c2667eb3 -r a70a7eebb435 macros.xml
--- a/macros.xml	Thu Mar 01 11:56:28 2018 -0500
+++ b/macros.xml	Wed May 16 17:31:03 2018 -0400
@@ -1,8 +1,8 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.5.2b">star</requirement>
-            <requirement type="package" version="0.1.19">samtools</requirement>
+            <requirement type="package" version="2.6.0b">star</requirement>
+            <requirement type="package" version="1.8">samtools</requirement>
         </requirements>
     </xml>
     <token name="@FASTQ_GZ_OPTION@">
diff -r 2055c2667eb3 -r a70a7eebb435 rg_rnaStar.xml
--- a/rg_rnaStar.xml	Thu Mar 01 11:56:28 2018 -0500
+++ b/rg_rnaStar.xml	Wed May 16 17:31:03 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rna_star" name="RNA STAR" version="2.5.2b-2" profile="17.01">
+<tool id="rna_star" name="RNA STAR" version="2.6.0b-1" profile="17.01">
     <description>Gapped-read mapper for RNA-seq data</description>
     <macros>
         <import>macros.xml</import>
@@ -92,8 +92,11 @@
         ## Output parameters
         #if str( $output_params.output_select ) == "yes":
             --outSAMattributes $output_params.outSAMattributes
-            --outSAMstrandField $output_params.outSAMstrandField
+            #if str( $params.settingsType ) != "star_fusion":
+                --outSAMstrandField $output_params.outSAMstrandField
+            #end if
             --outFilterIntronMotifs $output_params.outFilterIntronMotifs
+            --outFilterIntronStrands $output_params.outFilterIntronStrands
             #if str( $output_params.output_params2.output_select2 ) == "yes":
                 --outSAMunmapped $output_params.output_params2.outSAMunmapped
                 --outSAMprimaryFlag $output_params.output_params2.outSAMprimaryFlag
@@ -108,6 +111,9 @@
                 --outFilterScoreMinOverLread "$output_params.output_params2.outFilterScoreMinOverLread"
                 --outFilterMatchNmin "$output_params.output_params2.outFilterMatchNmin"
                 --outFilterMatchNminOverLread "$output_params.output_params2.outFilterMatchNminOverLread"
+                --outSAMmultNmax "$output_params.output_params2.outSAMmultNmax"
+                --outSAMtlen "$output_params.output_params2.outSAMtlen"
+                --outBAMsortingBinsN "$output_params.output_params2.outBAMsortingBinsN"
             #end if
         #end if
 
@@ -122,9 +128,9 @@
             --alignIntronMax 200000
             --twopassMode Basic
             --twopass1readsN -1
-
-            ## --chimSegmentReadGapMax 3              ## not an option in STAR 2.4.0
-            ## --alignSJstitchMismatchNmax 5 -1 5 5   ## not an option in STAR 2.4.0
+            --chimSegmentReadGapMax 3
+            --alignSJstitchMismatchNmax 5 -1 5 5
+            --outSAMstrandField intronMotif
 
         #elif str( $params.settingsType ) == "full":
             ## Extended parameter options
@@ -159,12 +165,16 @@
 
             ## Chimeric alignment parameter options
             #if str( $params.chim.chim_select ) == "yes":
+                --chimOutType Junctions SeparateSAMold
                 --chimSegmentMin "$params.chim.chimSegmentMin"
                 --chimScoreMin "$params.chim.chimScoreMin"
                 --chimScoreDropMax "$params.chim.chimScoreDropMax"
                 --chimScoreSeparation "$params.chim.chimScoreSeparation"
                 --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG"
                 --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin"
+                --chimMainSegmentMultNmax "$params.chim.chimMainSegmentMultNmax"
+                --chimMultimapNmax "$params.chim.chimMultimapNmax"
+                --chimMultimapScoreRange "$params.chim.chimMultimapScoreRange"
             #end if
 
             ## Limits
@@ -176,14 +186,9 @@
         #end if
 
     ## Convert chimeric reads.
-    #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0 ):
+    #if str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0:
         &&
-        samtools view
-            -@ \${GALAXY_SLOTS:-4}
-            -Shb Chimeric.out.sam |
-        
-        samtools sort
-            -@ \${GALAXY_SLOTS:-4} - ChimericSorted
+        samtools sort -@ \${GALAXY_SLOTS:-4} -o ChimericSorted.bam -O BAM Chimeric.out.sam
     #end if
     ]]></command>
 
@@ -269,6 +274,10 @@
                     <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option>
                     <option value="RemoveNoncanonicalUnannotated">Remove alignments with unannotated non-canonical junctions</option>
                 </param>
+                <param argument="--outFilterIntronStrands" type="select" label="Filter alignments containing junctions with inconsistent strands">
+                    <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">
@@ -290,6 +299,12 @@
                       <param argument="--outFilterScoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output"/>
                       <param argument="--outFilterMatchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output"/>
                       <param argument="--outFilterMatchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output"/>
+                      <param argument="--outSAMmultNmax" type="integer" value="-1" min="-1" label="Maximum number of multimapping alignments to output for a read" help="A value of -1 (the default) results in all alignments (up to –-outFilterMultimapNmax) being output" />
+                      <param argument="--outSAMtlen" type="select" label="Calculation method for TLEN">
+                          <option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option>
+                          <option value="2">leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends</option>
+                      </param>
+                      <param argument="--outBAMsortingBinsN" type="integer" value="50" min="1" label="Number of genome bins for coordinate-sorting" help="Higher values result in lower RAM requirements during the sorting step. The default value is 50."/>
                   </when>
                   <when value="no"/>
               </conditional>
@@ -358,6 +373,9 @@
                         <param argument="--chimScoreSeparation" type="integer" min="0" value="10" label="Minimum difference between the best chimeric score and the next one"/>
                         <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1" label="Penalty for a non-GT/AG chimeric junction"/>
                         <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction"/>
+                        <param argument="--chimMainSegmentMultNmax" type="integer" min="1" value="10" label="Maximum number of multi-alignments for the main chimeric segment." help="A value of 1 prohibits multimapping main segments"/>
+                        <param argument="--chimMultimapNmax" type="integer" min="0" value="0" label="Maximum number of chimeric multi-alignments" help="A value of 0 (the default) only considers unique alignments" />
+                        <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1" label="Score range for multi-mapping chimeras" help="The threshold below the best chimeric score that a multimapping chimera must have to be output. This is ignored unless --chimMultimapNmax is above 1" />
                     </when>
                     <when value="no"/>
                 </conditional>
@@ -389,7 +407,7 @@
         </data>
 
         <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam">
-            <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )</filter>
+            <filter>params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0</filter>
             <actions>
                 <conditional name="refGenomeSource.geneSource">
                     <when value="indexed">
@@ -581,10 +599,7 @@
 **STAR-Fusion**
 
 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::
-
-  --chimSegmentReadGapMax 3             # not an option in STAR 2.4.0
-  --alignSJstitchMismatchNmax 5 -1 5 5  # not an option in STAR 2.4.0
+STAR prior to STAR-Fusion can be pre-selected.
 
 **Attributions**
 
diff -r 2055c2667eb3 -r a70a7eebb435 test-data/rnastar_test2_mapped_reads.bam
Binary file test-data/rnastar_test2_mapped_reads.bam has changed
diff -r 2055c2667eb3 -r a70a7eebb435 test-data/rnastar_test_mapped_reads.bam
Binary file test-data/rnastar_test_mapped_reads.bam has changed