Mercurial > repos > artbio > lumpy_smoove
changeset 4:49da975ba395 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
| author | artbio |
|---|---|
| date | Thu, 27 Aug 2020 17:14:25 -0400 |
| parents | 65b400409455 |
| children | bd4135caa3fa |
| files | lumpy_smoove.xml test-data/result-5.vcf |
| diffstat | 2 files changed, 100 insertions(+), 15 deletions(-) [+] |
line wrap: on
line diff
--- a/lumpy_smoove.xml Wed Aug 26 12:24:07 2020 -0400 +++ b/lumpy_smoove.xml Thu Aug 27 17:14:25 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="lumpy_smoove" name="lumpy_smoove" version="0.5.0"> +<tool id="lumpy_smoove" name="lumpy_smoove" version="0.6.0"> <description>find structural variants using the smoove workflow</description> <macros> <import>macro_lumpy_smoove.xml</import> @@ -12,10 +12,15 @@ <command detect_errors="exit_code"><![CDATA[ @pipefail@ @set_fasta_index@ - ln -s $normal_bam normal.bam && - ln -s $tumor_bam tumor.bam && - samtools index -@ \${GALAXY_SLOTS:-4} normal.bam && - samtools index -@ \${GALAXY_SLOTS:-4} tumor.bam && + #if $set_plan.plan_choice=='pair': + ln -s $set_plan.normal_bam normal.bam && + ln -f -s $set_plan.normal_bam.metadata.bam_index normal.bam.bai && + ln -s $set_plan.tumor_bam tumor.bam && + ln -f -s $set_plan.tumor_bam.metadata.bam_index tumor.bam.bai && + #else + ln -s $set_plan.single_bam single.bam && + ln -f -s $set_plan.single_bam.metadata.bam_index single.bam.bai && + #end if smoove call --name output #if $set_exclusion.choices=="yes": @@ -27,15 +32,28 @@ #if $prpos=="no": --removepr #end if - normal.bam tumor.bam && + *.bam && ls -latr && gunzip output-smoove.genotyped.vcf.gz ]]></command> <inputs> <expand macro="reference_source_conditional" /> - <param format="bam" name="normal_bam" type="data" label="BAM alignments from the normal sample"/> - <param format="bam" name="tumor_bam" type="data" label="BAM alignments from the tumor sample"/> + <conditional name="set_plan"> + <param name="plan_choice" type="select" label="Analyse a single Bam or a pair of Bam (eg normal/tumor)" display="radio"> + <option value="pair" selected="true">A pair of Bam files</option> + <option value="single">A single Bam</option> + </param> + <when value="pair"> + <param format="bam" name="normal_bam" type="data" label="BAM alignment from the normal sample"/> + <param format="bam" name="tumor_bam" type="data" label="BAM alignment from the tumor sample"/> + </when> + <when value="single"> + <param format="bam" name="single_bam" type="data" label="BAM alignment from a single sample"/> + </when> + </conditional> + + <conditional name="set_exclusion"> <param name="choices" type="select" label="exclude regions with a bed file" display="radio"> <option value="no" selected="true">No</option> @@ -66,7 +84,7 @@ <param name="choices" value="yes"/> <param name="bedmask" value="exclude.bed"/> <param name="prpos" value="no"/> - <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="6"/> + <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="8"/> </test> <test> <param name="reference_source_selector" value="history" /> @@ -75,7 +93,7 @@ <param name="tumor_bam" value="celegans_RG_2.bam"/> <param name="choices" value="no"/> <param name="prpos" value="no"/> - <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="6"/> + <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="8"/> </test> <test> <param name="reference_source_selector" value="history" /> @@ -84,7 +102,7 @@ <param name="tumor_bam" value="celegans_RG_1.bam"/> <param name="choices" value="no"/> <param name="prpos" value="no"/> - <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="6"/> + <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="8"/> </test> <test> <param name="reference_source_selector" value="history" /> @@ -93,9 +111,17 @@ <param name="tumor_bam" value="celegans_RG_2.bam"/> <param name="choices" value="no"/> <param name="prpos" value="yes"/> - <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="6"/> + <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="8"/> </test> - + <test> + <param name="reference_source_selector" value="history" /> + <param name="plan_choice" value="single" /> + <param name="ref_file" value="chrI-ce11.fa"/> + <param name="single_bam" value="celegans_RG_1.bam"/> + <param name="choices" value="no"/> + <param name="prpos" value="no"/> + <output name="vcf_call" ftype="vcf" file="result-5.vcf" lines_diff="8"/> + </test> </tests> <help> @@ -144,12 +170,13 @@ **Input(s)** -* BAM files: One Bam for normal sample and one Bam for tumor sample. Only BAM alignments produced by BWA-mem have been tested with this tool +* BAM files: Either a pair of Bam files (e.g. normal vs tumor sample) or a single Bam file. + Only BAM alignments produced by BWA-mem have been tested with this tool .. class:: warningmark It is mandatory for proper run of svtyper that **BAM files contain read group information**, - ie the @RG tag is present and filled in each BAM + ie the @RG tag is present and filled in each BAM file * A bed file describing the regions to exclude from the analysis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result-5.vcf Thu Aug 27 17:14:25 2020 -0400 @@ -0,0 +1,58 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##fileDate=20200827 +##reference=reference.fa +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> +##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> +##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> +##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> +##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> +##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> +##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> +##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> +##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> +##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> +##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> +##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> +##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> +##ALT=<ID=DEL,Description="Deletion"> +##ALT=<ID=DUP,Description="Duplication"> +##ALT=<ID=INV,Description="Inversion"> +##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> +##ALT=<ID=INS,Description="Insertion of novel sequence"> +##ALT=<ID=CNV,Description="Copy number variable region"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> +##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> +##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> +##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> +##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations"> +##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)"> +##contig=<ID=chrI,length=15072434> +##smoove_version=0.2.5 +##smoove_count_stats=celegans-1:2869,2691,202,330 +##source=LUMPY +##bcftools_annotateVersion=1.10.2+htslib-1.10.2 +##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Thu Aug 27 18:59:21 2020 +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##bcftools_viewVersion=1.10.2+htslib-1.10.2 +##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Thu Aug 27 18:59:21 2020 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT celegans-1 +chrI 10416569 1 N <DUP> 130.28 . SVTYPE=DUP;SVLEN=981;END=10417550;STRANDS=-+:4;IMPRECISE;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;SU=4;PE=4;SR=0;AC=2;AN=2 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:16:130.28:-15,-4,-2:14:4:9:4:9:0:0:0:4:9:0.69