Mercurial > repos > iuc > rgrnastar
changeset 28:3e94726bfa9d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
| author | iuc |
|---|---|
| date | Sun, 11 Feb 2024 00:01:54 +0000 |
| parents | 79de45b5069b |
| children | b0f2be869d6d |
| files | macros.xml rg_rnaStar.xml test-data/rnastar_test_diploid.log test-data/rnastar_test_mapped_reads.vcf test-data/rnastar_test_mapped_reads_diploid.bam test-data/rnastar_test_mapped_reads_test10.bam test-data/rnastar_test_splicejunctions_diploid.bed |
| diffstat | 7 files changed, 126 insertions(+), 6 deletions(-) [+] |
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--- a/macros.xml Fri Sep 01 13:17:29 2023 +0000 +++ b/macros.xml Sun Feb 11 00:01:54 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))
--- a/rg_rnaStar.xml Fri Sep 01 13:17:29 2023 +0000 +++ b/rg_rnaStar.xml Sun Feb 11 00:01:54 2024 +0000 @@ -91,6 +91,15 @@ ## Read MAPQ --outSAMmapqUnique ${oformat.outSAMmapqUnique} + ## Transform diploid mode output to reference coordinates + #if str($refGenomeSource.geneSource) == 'history': + #if 'diploidconditional' in $refGenomeSource: + #if str($refGenomeSource.diploidconditional.diploid) == 'Yes': + '${refGenomeSource.diploidconditional.genomeTransformOutput}' + #end if + #end if + #end if + ## Output filter parameters ## Basic Filters @@ -318,6 +327,18 @@ <expand macro="quantModeNoGTF" /> </when> </conditional> + <conditional name="diploidconditional"> + <param name="diploid" type="select" label="Diploid mode" help="Map RNA-seq reads to a diploid genome"> + <option value="No" selected="True">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param argument="--genomeTransformVCF" type="data" format="vcf" label="VCF file with diploid SNVs and InDels" help="The homozygous and heterozygous alleles from this VCF will be inserted into the reference genome to create a transformed genome with two haplotypes"/> + <param argument="--genomeTransformOutput" type="boolean" checked="false" truevalue="--genomeTransformOutput SAM SJ Quant" falsevalue="--genomeTransformOutput None" label="Transform alignments, spliced junctions and quantifications back to the reference coordinates" help="Use this if downstream processing relies on reference coordinates"/> + </when> + <when value="No"> + </when> + </conditional> </when> </conditional> @@ -810,6 +831,7 @@ <output name="chimeric_junctions" file="test3.chimjunc.tabular" compare="diff" lines_diff="2"/> </test> + <!-- test 10 --> <test expect_num_outputs="3"> <conditional name="singlePaired"> <param name="sPaired" value="single" /> @@ -837,7 +859,7 @@ <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="mapped_reads" file="rnastar_test_mapped_reads_test10.bam" compare="sim_size" delta="634" /> </test> <!-- twopass mode tests --> <!-- test Basic twopass --> @@ -1117,6 +1139,28 @@ <output name="signal_unique_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" /> <output name="signal_uniquemultiple_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" /> </test> + <!-- test diploid mode --> + <test expect_num_outputs="3"> + <conditional name="singlePaired"> + <param name="sPaired" value="single" /> + <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> + </conditional> + <conditional name="refGenomeSource"> + <param name="geneSource" value="history" /> + <param name="genomeFastaFiles" value="tophat_test.fa.gz" /> + <param name="genomeSAindexNbases" value="5" /> + </conditional> + <conditional name="diploidconditional"> + <param name="diploid" value="Yes" /> + <!-- generated from rnastar_test_mapped_reads.bam with + bcftools mpileup and bcftools call --> + <param name="genomeTransformVCF" value="rnastar_test_mapped_reads.vcf" ftype="vcf" /> + <param name="genomeTransformOutput" value="true" /> + </conditional> + <output name="output_log" file="rnastar_test_diploid.log" compare="re_match_multiline" /> + <output name="splice_junctions" file="rnastar_test_splicejunctions_diploid.bed"/> + <output name="mapped_reads" file="rnastar_test_mapped_reads_diploid.bam" compare="sim_size" delta="634" /> + </test> </tests> <help><![CDATA[ **What it does**
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_diploid.log Sun Feb 11 00:01:54 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%
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_mapped_reads.vcf Sun Feb 11 00:01:54 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