# HG changeset patch
# User iuc
# Date 1707609750 0
# Node ID 8dc4a444ec042a0edc71f9b3aa33b5a188c5ecfb
# Parent  5ef7ec16b04f28d7156949e9858f90119dece81d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f

diff -r 5ef7ec16b04f -r 8dc4a444ec04 macros.xml
--- a/macros.xml	Fri Sep 01 13:18:03 2023 +0000
+++ b/macros.xml	Sun Feb 11 00:02:30 2024 +0000
@@ -4,8 +4,8 @@
     The data manager uses a symlink to this macro file to keep the STAR and
     the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
     <!-- STAR version to be used -->
-    <token name="@TOOL_VERSION@">2.7.10b</token>
-    <token name="@VERSION_SUFFIX@">4</token>
+    <token name="@TOOL_VERSION@">2.7.11a</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <!-- STAR index version compatible with this version of STAR
     This is the STAR version that introduced the index structure expected
@@ -15,14 +15,14 @@
     or by looking for the versionGenome parameter in source/parametersDefault
     of STAR's source code -->
     <token name="@IDX_VERSION@">2.7.4a</token>
-    <token name="@IDX_VERSION_SUFFIX@">1</token>
+    <token name="@IDX_VERSION_SUFFIX@">0</token>
     <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
 
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">star</requirement>
-            <requirement type="package" version="1.16.1">samtools</requirement>
-            <requirement type="package" version="1.12">gzip</requirement>
+            <requirement type="package" version="1.18">samtools</requirement>
+            <requirement type="package" version="1.13">gzip</requirement>
             <yield />
         </requirements>
     </xml>
@@ -122,6 +122,13 @@
             #if str($refGenomeSource.genomeSAindexNbases):
                 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
             #end if
+            ## Diploid mode
+            #if 'diploidconditional' in $refGenomeSource:
+                #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
+                    --genomeTransformVCF '${refGenomeSource.diploidconditional.genomeTransformVCF}'
+                    --genomeTransformType Diploid
+                #end if   
+            #end if
             --runThreadN \${GALAXY_SLOTS:-4}
             ## in bytes
             --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
diff -r 5ef7ec16b04f -r 8dc4a444ec04 test-data/rnastar_test_diploid.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnastar_test_diploid.log	Sun Feb 11 00:02:30 2024 +0000
@@ -0,0 +1,37 @@
+                                 Started job on |	.*
+                             Started mapping on |	.*
+                                    Finished on |	.*
+       Mapping speed, Million of reads per hour |	inf
+
+                          Number of input reads |	100
+                      Average input read length |	75
+                                    UNIQUE READS:
+                   Uniquely mapped reads number |	100
+                        Uniquely mapped reads % |	100.00%
+                          Average mapped length |	74.65
+                       Number of splices: Total |	53
+            Number of splices: Annotated (sjdb) |	0
+                       Number of splices: GT/AG |	53
+                       Number of splices: GC/AG |	0
+                       Number of splices: AT/AC |	0
+               Number of splices: Non-canonical |	0
+                      Mismatch rate per base, % |	1.63%
+                         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 |	0
+             % of reads mapped to multiple loci |	0.00%
+        Number of reads mapped to too many loci |	0
+             % of reads mapped to too many loci |	0.00%
+                                  UNMAPPED READS:
+  Number of reads unmapped: too many mismatches |	0
+       % of reads unmapped: too many mismatches |	0.00%
+            Number of reads unmapped: too short |	0
+                 % of reads unmapped: too short |	0.00%
+                Number of reads unmapped: other |	0
+                     % of reads unmapped: other |	0.00%
+                                  CHIMERIC READS:
+                       Number of chimeric reads |	0
+                            % of chimeric reads |	0.00%
diff -r 5ef7ec16b04f -r 8dc4a444ec04 test-data/rnastar_test_mapped_reads.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnastar_test_mapped_reads.vcf	Sun Feb 11 00:02:30 2024 +0000
@@ -0,0 +1,30 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##bcftoolsVersion=1.13+htslib-1.13+ds
+##bcftoolsCommand=mpileup -Ob -o rnastar_test_mapped_reads.bcf -f tophat_test.fa rnastar_test_mapped_reads.bam
+##reference=file://tophat_test.fa
+##contig=<ID=test_chromosome,length=650>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Read Position Bias (closer to 0 is better)">
+##INFO=<ID=MQBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Mapping Quality Bias (closer to 0 is better)">
+##INFO=<ID=BQBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Base Quality Bias (closer to 0 is better)">
+##INFO=<ID=MQSBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Mapping Quality vs Strand Bias (closer to 0 is better)">
+##INFO=<ID=SCBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Soft-Clip Length Bias (closer to 0 is better)">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
+##bcftools_callVersion=1.13+htslib-1.13+ds
+##bcftools_callCommand=call -vmO z -o rnastar_test_mapped_reads.vcf.gz rnastar_test_mapped_reads.bcf; Date=Tue Jan  2 11:53:57 2024
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	rnastar_test_mapped_reads.bam
+test_chromosome	219	.	G	C	170.416	.	DP=27;VDB=0.505999;SGB=-0.693021;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,7,20;MQ=20	GT:PL	1/1:200,81,0
diff -r 5ef7ec16b04f -r 8dc4a444ec04 test-data/rnastar_test_mapped_reads_diploid.bam
Binary file test-data/rnastar_test_mapped_reads_diploid.bam has changed
diff -r 5ef7ec16b04f -r 8dc4a444ec04 test-data/rnastar_test_mapped_reads_test10.bam
Binary file test-data/rnastar_test_mapped_reads_test10.bam has changed
diff -r 5ef7ec16b04f -r 8dc4a444ec04 test-data/rnastar_test_splicejunctions_diploid.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnastar_test_splicejunctions_diploid.bed	Sun Feb 11 00:02:30 2024 +0000
@@ -0,0 +1,2 @@
+test_chromosome	251	350	1	1	0	27	0	37
+test_chromosome	401	500	1	1	0	25	0	36