# HG changeset patch
# User iuc
# Date 1667321815 0
# Node ID 980d2a2e11809f65fc6f19ea3df18531e1670344
# Parent  4074fc1940e221d7e4923a88ddf3282d1632a3ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb

diff -r 4074fc1940e2 -r 980d2a2e1180 rg_rnaStar.xml
--- a/rg_rnaStar.xml	Fri Sep 10 16:45:37 2021 +0000
+++ b/rg_rnaStar.xml	Tue Nov 01 16:56:55 2022 +0000
@@ -1,13 +1,13 @@
-<tool id="rna_star" name="RNA STAR" version="@VERSION@+galaxy0" profile="20.01" license="MIT">
+<tool id="rna_star" name="RNA STAR" version="@VERSION@+galaxy1" profile="20.01" license="MIT">
     <description>Gapped-read mapper for RNA-seq data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam"/>
     <xrefs>
         <xref type="bio.tools">star</xref>
     </xrefs>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <expand macro="requirements"/>
-    <expand macro="edam"/>
     <expand macro="stdio" />
 
 <!--
@@ -145,6 +145,19 @@
             --chimMultimapScoreRange 10
             --chimMultimapNmax 10
             --chimNonchimScoreDropMin 10
+        
+        #elif str( $algo.params.settingsType ) == 'arriba':
+            ## Preset parameters for Arriba
+            --peOverlapNbasesMin 10
+            --alignSplicedMateMapLminOverLmate 0.5
+            --alignSJstitchMismatchNmax 5 -1 5 5
+            --chimSegmentMin 10
+            --chimJunctionOverhangMin 10
+            --chimScoreDropMax 30
+            --chimScoreJunctionNonGTAG 0
+            --chimScoreSeparation 1
+            --chimSegmentReadGapMax 3
+            --chimMultimapNmax 50
 
         #elif str( $algo.params.settingsType ) == 'full':
             ## Extended parameter options
@@ -163,6 +176,7 @@
             --alignIntronMax ${algo.params.align.alignIntronMax}
             --alignMatesGapMax ${algo.params.align.alignMatesGapMax}
             --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin}
+            --alignSJstitchMismatchNmax ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax1} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax2} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax3} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax4}
             --alignSJDBoverhangMin ${algo.params.align.alignSJDBoverhangMin}
             --alignSplicedMateMapLmin ${algo.params.align.alignSplicedMateMapLmin}
             --alignSplicedMateMapLminOverLmate ${algo.params.align.alignSplicedMateMapLminOverLmate}
@@ -349,7 +363,9 @@
             <option value="">Don't report chimeric alignments</option>
             <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option>
             <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option>
-            <option value="WithinBAM Junctions">In both forms (WithinBAM Junctions)</option>
+            <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option>
+            <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option>
+            <option value="WithinBAM Junctions">Deprecated: In both forms (WithinBAM Junctions)</option>
         </param>
 
         <section name="oformat" title="BAM output format specification" expanded="true">
@@ -433,11 +449,13 @@
                 <param name="settingsType" type="select" label="Configure seed, alignment and limits options">
                     <option value="default" selected="true">Use Defaults</option>
                     <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
+                    <option value="arriba">Use parameters suggested for Arriba</option>
                     <option value="full">Extended parameter list</option>
                 </param>
                 <when value="default"/>
                 <!-- Set STAR-fusion parameters in command section -->
                 <when value="star_fusion"/>
+                <when value="arriba"/>
 
                 <when value="full">
                     <section name="seed" title="Seed parameters" expanded="false">
@@ -455,6 +473,12 @@
                         <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
                         <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
                         <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
+                        <section name="alignSJstitchMismatchNmax" title="Maximum number of mismatches for stitching of the splice junctions (-1: no limit)" expanded="true">
+                            <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax1" type="integer" min="-1" value="0" label="Non-canonical motifs"/>
+                            <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax2" type="integer" min="-1" value="-1" label="GT/AG and CT/AC motif"/>
+                            <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax3" type="integer" min="-1" value="0" label="GC/AG and CT/GC motif"/>
+                            <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax4" type="integer" min="-1" value="0" label="AT/AC and GT/AT motif"/>
+                        </section>
                         <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>
                         <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
                         <param argument="--alignSplicedMateMapLminOverLmate" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length"/>
@@ -654,7 +678,7 @@
             <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
             <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
             <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
-            <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" />
+            <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" />
         </test>
         <test expect_num_outputs="3">
             <conditional name="singlePaired">
@@ -989,6 +1013,23 @@
 - under *Algorithmic settings*, **Configure seed, alignment and limits options**:
   `use parameters suggested for STAR-Fusion`.
 
+*Arriba*
+
+Arriba_ can use the BAM with chimeric junctions or both files separately, generated by STAR, as input, but you
+need to enable **chimeric alignment detection** by STAR for those datasets to be
+generated. Hence, be sure to select either:
+
+**Report chimeric alignments?**: `As separate tabular "Junctions" output (Junctions)` or **Report chimeric alignments?**: `Within the BAM output (together with regular alignments; WithinBAM)`.
+
+In addition, the following parameters_ related to chimeric alignment are recommended for improved sensitivity
+
+- under *Output filter criteria*,
+  **Would you like to set additional output filters?**: select `Yes' to set 
+  **Maximum number of alignments to output a read's alignment results, plus 1** to 50 
+
+- under *Algorithmic settings*, **Configure seed, alignment and limits options**:
+  `use parameters suggested for Arriba`.
+
 *Cufflinks*
 
 .. class:: infomark
@@ -1019,7 +1060,9 @@
 
 .. _STAR: https://github.com/alexdobin/STAR
 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
+.. _Arriba: https://github.com/suhrig/arriba
 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-kickstart-mode-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs
+.. _parameters: https://arriba.readthedocs.io/en/latest/workflow/
     ]]></help>
     <expand macro="citations"/>
 </tool>