| Previous changeset 0:00cab3d2e98b (2018-08-15) Next changeset 2:103a769fe8d2 (2018-10-12) |
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Commit message:
planemo upload commit c214e5fa219f8d3593ac8aad9e15f9eeba5320f5 |
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modified:
svtyper.xml |
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added:
README.md test-data/test2.out.vcf |
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| diff -r 00cab3d2e98b -r 2ba5317566c0 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Oct 12 13:48:00 2018 -0400 |
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| @@ -0,0 +1,17 @@ +# svtyper galaxy tool wrapper + +## About + +This is a galaxy tool wrapper written for svtyper, which can be found here: + +https://github.com/hall-lab/svtyper + +Issues with the wrapper can be submitted here in this repo. Issues with svtyper should be submitted to the svtyper developers at: + +https://github.com/hall-lab/svtyper/issues + +## Install + +This wrapper is available for install via the main galaxy tool shed: + +https://toolshed.g2.bx.psu.edu \ No newline at end of file |
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| diff -r 00cab3d2e98b -r 2ba5317566c0 svtyper.xml --- a/svtyper.xml Wed Aug 15 15:40:54 2018 -0400 +++ b/svtyper.xml Fri Oct 12 13:48:00 2018 -0400 |
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| @@ -103,6 +103,7 @@ <param name="libin" label="Library json file" argument="--lib_info" + optional="true" type="data" format="json" @@ -201,6 +202,13 @@ <output name="vcfout" file="test1.out.vcf" compare="diff" lines_diff="2" /> </test> + <test> + <!-- Test no input json lib file --> + <param name="vcf" value="test1.vcf"/> + <param name="alignment_files" value="test1.bam"/> + <output name="vcfout" file="test2.out.vcf" + compare="diff" lines_diff="2" /> + </test> </tests> <help> <![CDATA[ |
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| diff -r 00cab3d2e98b -r 2ba5317566c0 test-data/test2.out.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.out.vcf Fri Oct 12 13:48:00 2018 -0400 |
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| b'@@ -0,0 +1,354 @@\n+##fileformat=VCFv4.1\n+##fileDate=20181012\n+##reference=/shared/genomes/b37/full/human_g1k_v37.fasta\n+##INFO=<ID=TOOL,Number=1,Type=String,Description="Tool used to generate variant call">\n+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">\n+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">\n+##INFO=<ID=STR,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format">\n+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">\n+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">\n+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">\n+##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">\n+##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">\n+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">\n+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">\n+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">\n+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">\n+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">\n+##INFO=<ID=SUP,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">\n+##INFO=<ID=PESUP,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">\n+##INFO=<ID=SRSUP,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">\n+##INFO=<ID=EVTYPE,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">\n+##INFO=<ID=PRIN,Number=0,Type=Flag,Description="Indicates variant as the principal variant in a BEDPE pair">\n+##ALT=<ID=DEL,Description="Deletion">\n+##ALT=<ID=DUP,Description="Duplication">\n+##ALT=<ID=INV,Description="Inversion">\n+##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">\n+##ALT=<ID=INS,Description="Insertion of novel sequence">\n+##ALT=<ID=CNV,Description="Copy number variable region">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=SUP,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">\n+##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">\n+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">\n+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">\n+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">\n+##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">\n+##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood form imprecise events">\n+##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel">\n+##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">\n+##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancest'..b'PESUP=103;SRSUP=0;EVTYPE=PE;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:16:64:60:3:0.10:-2,-3,-7:60:3:0:0:0:60:3:0.048\n+3\t187732908\t212594\tA\t<DEL>\t224.62\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-1909;END=187734817;STR=+-:118;IMPRECISE;CIPOS=-2,8;CIEND=-10,1;EVENT=212594;SUP=118;PESUP=118;SRSUP=0;EVTYPE=PE;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:200:56:42:13:224.62:-27,-4,-30:42:13:0:0:0:42:13:0.24\n+3\t189224507\t213103\tC\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-874;END=189225381;STR=+-:9;CIPOS=0,0;CIEND=0,0;EVENT=213103;SUP=9;PESUP=1;SRSUP=8;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:200:161:161:0:0.00:-0,-48,-160:160:0:76:0:0:84:0:0\n+3\t189363422\t213158\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-7487;END=189370909;STR=+-:132;IMPRECISE;CIPOS=-1,11;CIEND=0,0;EVENT=213158;SUP=132;PESUP=132;SRSUP=0;EVTYPE=PE;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:200:129:129:0:0.00:-0,-39,-128:128:0:58:0:0:70:0:0\n+3\t190478458\t213572\tT\t<DEL>\t768.10\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-175;END=190478633;STR=+-:151;CIPOS=0,0;CIEND=0,0;EVENT=213572;SUP=151;PESUP=10;SRSUP=141;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t1/1:66:26:0:26:768.10:-78,-8,-1:0:26:0:16:9:0:0:1\n+3\t192673320\t214366\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-66;END=192673386;STR=+-:108;CIPOS=0,0;CIEND=0,0;EVENT=214366;SUP=108;PESUP=1;SRSUP=107;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:200:70:70:0:0.00:-0,-21,-70:70:0:70:0:0:0:0:0\n+3\t192744355\t214380\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-537;END=192744892;STR=+-:229;CIPOS=0,0;CIEND=0,0;EVENT=214380;SUP=229;PESUP=217;SRSUP=12;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:200:121:121:0:0.00:-0,-36,-120:120:0:55:0:0:65:0:0\n+3\t192875332\t214421\tT\t<DEL>\t824.15\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-10072;END=192885404;STR=+-:734;CIPOS=0,0;CIEND=0,0;EVENT=214421;SUP=734;PESUP=499;SRSUP=235;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:200:118:77:40:824.15:-86,-4,-47:76:39:39:12:2:37:24:0.34\n+3\t194398752\t214899\tC\t<DEL>\t954.46\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-1548;END=194400300;STR=+-:293;IMPRECISE;CIPOS=-1,2;CIEND=0,0;EVENT=214899;SUP=293;PESUP=293;SRSUP=0;EVTYPE=PE;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t1/1:51:40:5:34:954.46:-96,-6,-1:5:34:0:0:0:5:34:0.87\n+3\t195457294\t215225\tG\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-13713;END=195471007;STR=+-:71;IMPRECISE;CIPOS=-2,9;CIEND=0,0;EVENT=215225;SUP=71;PESUP=71;SRSUP=0;EVTYPE=PE;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:200:127:127:0:0.00:-0,-38,-126:126:0:61:0:0:65:0:0\n+3\t195569217\t215275\tG\t<DEL>\t479.42\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-724;END=195569941;STR=+-:385;CIPOS=0,0;CIEND=0,0;EVENT=215275;SUP=385;PESUP=362;SRSUP=23;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:200:83:57:25:479.42:-52,-4,-37:56:24:23:0:2:33:21:0.3\n+3\t195949296\t215374\tA\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-2004;END=195951300;STR=+-:229;IMPRECISE;CIPOS=-1,3;CIEND=0,0;EVENT=215374;SUP=229;PESUP=229;SRSUP=0;EVTYPE=PE;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:200:129:129:0:0.00:-0,-39,-128:128:0:53:0:0:75:0:0\n+3\t196934573\t215670\tA\t<DEL>\t920.21\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-4681;END=196939254;STR=+-:349;CIPOS=0,0;CIEND=0,0;EVENT=215670;SUP=349;PESUP=259;SRSUP=90;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:200:106:63:42:920.21:-94,-2,-35:62:41:27:9:3:35:28:0.4\n+2\t84728755\t894054_1\tA\tA]15:89212842]\t65.75\t.\tTOOL=LUMPY;SVTYPE=BND;STR=++:74;IMPRECISE;CIPOS=-1,2;CIEND=0,0;MATEID=894054_2;EVENT=894054;SUP=74;PESUP=73;SRSUP=1;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:65:39:32:6:65.75:-12,-5,-26:32:6:0:0:0:32:6:0.16\n+15\t89212842\t894054_2\tC\tC]2:84728755]\t65.75\t.\tTOOL=LUMPY;SVTYPE=BND;STR=++:74;IMPRECISE;CIPOS=0,0;CIEND=-1,2;MATEID=894054_1;EVENT=894054;SUP=74;PESUP=73;SRSUP=1;EVTYPE=PE,SR\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:65:39:32:6:65.75:-12,-5,-26:32:6:0:0:0:32:6:0.16\n' 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