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changeset 3:da5aae7550b3 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
author artbio
date Thu, 07 May 2020 19:38:14 -0400
parents 6059f4cb4cf2
children 093bb151a0a8
files lumpy.xml test-data/output_two.paired_end.vcf test-data/sample_Del.bam test-data/sample_cle.bam
diffstat 4 files changed, 53 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/lumpy.xml	Mon Oct 14 07:12:01 2019 -0400
+++ b/lumpy.xml	Thu May 07 19:38:14 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="lumpy" name="lumpy-sv" version="1.1.0">
+<tool id="lumpy" name="lumpy-sv" version="1.2.0">
     <description>find structural variants</description>
     <requirements>
         <requirement type="package" version="0.2.13">lumpy-sv</requirement>
@@ -153,7 +153,7 @@
         <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.bam">
             <filter>seq_method['seq_method_list'] == "paired-end"</filter>
         </data>
-        <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.B.bam">
+        <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.B.discordants.bam">
             <filter>seq_method['seq_method_list'] == "paired-end"</filter>
             <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
         </data>
@@ -166,6 +166,18 @@
 
     <tests>
         <test>
+            <param name="analysis_type_list" value="two_sample" />
+            <param name="input_file" value="sample_Del.bam" ftype="bam"/>
+            <param name="input_fileB" value="sample_cle.bam" ftype="bam"/>
+            <param name="seq_method_list" value="paired-end" />
+            <param name="mw" value="4"/>
+            <param name="tt" value="0"/>
+            <param name="back_distance" value="10"/>
+            <param name="weight" value="1" />
+            <param name="min_mapping_threshold" value="20" />
+            <output name="vcf_call" file="output_two.paired_end.vcf" ftype="vcf"/>
+        </test>
+        <test>
             <param name="analysis_type_list" value="one_sample" />
             <param name="input_file" value="sr.input.bam" ftype="bam"/>
             <param name="seq_method_list" value="single-read" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_two.paired_end.vcf	Thu May 07 19:38:14 2020 -0400
@@ -0,0 +1,39 @@
+##fileformat=VCFv4.2
+##source=LUMPY
+##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">
+##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
+##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
+##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">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	inputA.bam	inputB.bam
+22	23289741	1_1	N	N[9:130703751[	.	.	SVTYPE=BND;STRANDS=+-:8;EVENT=1;MATEID=1_2;CIPOS=-5,4;CIEND=-5,9;CIPOS95=0,0;CIEND95=0,0;SU=8;PE=1;SR=7;PRPOS=2.51045e-16,3.97879e-13,6.30596e-10,9.99428e-07,0.00158399,0.996836,0.00157659,2.48311e-06,3.9272e-09,6.20457e-12;PREND=9.46531e-15,5.9925e-12,3.81943e-09,2.43414e-06,0.00154348,0.988348,0.0100041,0.000100524,1.00845e-06,1.0173e-08,1.03097e-10,1.648e-13,2.63008e-16,4.19721e-19,6.68765e-22	GT:SU:PE:SR	./.:8:1:7	./.:0:0:0
+9	130703751	1_2	N	]22:23289741]N	.	.	SVTYPE=BND;STRANDS=-+:8;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=-5,9;CIEND=-5,4;CIPOS95=0,0;CIEND95=0,0;SU=8;PE=1;SR=7;PRPOS=9.46531e-15,5.9925e-12,3.81943e-09,2.43414e-06,0.00154348,0.988348,0.0100041,0.000100524,1.00845e-06,1.0173e-08,1.03097e-10,1.648e-13,2.63008e-16,4.19721e-19,6.68765e-22;PREND=2.51045e-16,3.97879e-13,6.30596e-10,9.99428e-07,0.00158399,0.996836,0.00157659,2.48311e-06,3.9272e-09,6.20457e-12	GT:SU:PE:SR	./.:8:1:7	./.:0:0:0
+22	23289769	2_1	N	]9:130703785]N	.	.	SVTYPE=BND;STRANDS=-+:6;EVENT=2;MATEID=2_2;CIPOS=-10,9;CIEND=-8,6;CIPOS95=0,0;CIEND95=0,0;SU=6;PE=1;SR=5;PRPOS=9.56458e-21,9.57993e-19,9.63619e-17,9.66176e-15,9.68222e-13,9.70268e-11,9.73337e-09,9.75383e-07,9.8152e-05,0.00983566,0.986124,0.00392583,1.5629e-05,6.22202e-08,2.47703e-10,9.86124e-13,3.92583e-15,1.5629e-17,6.22202e-20,2.47703e-22;PREND=1.04138e-16,1.03354e-14,1.02805e-12,1.02099e-10,1.01393e-08,1.00531e-06,9.91976e-05,0.00983351,0.980214,0.00975509,9.63746e-05,9.49631e-07,9.44926e-09,9.35516e-11,9.26106e-13	GT:SU:PE:SR	./.:6:1:5	./.:0:0:0
+9	130703785	2_2	N	N[22:23289769[	.	.	SVTYPE=BND;STRANDS=+-:6;SECONDARY;EVENT=2;MATEID=2_1;CIPOS=-8,6;CIEND=-10,9;CIPOS95=0,0;CIEND95=0,0;SU=6;PE=1;SR=5;PRPOS=1.04138e-16,1.03354e-14,1.02805e-12,1.02099e-10,1.01393e-08,1.00531e-06,9.91976e-05,0.00983351,0.980214,0.00975509,9.63746e-05,9.49631e-07,9.44926e-09,9.35516e-11,9.26106e-13;PREND=9.56458e-21,9.57993e-19,9.63619e-17,9.66176e-15,9.68222e-13,9.70268e-11,9.73337e-09,9.75383e-07,9.8152e-05,0.00983566,0.986124,0.00392583,1.5629e-05,6.22202e-08,2.47703e-10,9.86124e-13,3.92583e-15,1.5629e-17,6.22202e-20,2.47703e-22	GT:SU:PE:SR	./.:6:1:5	./.:0:0:0
+22	23292033	3_1	N	]9:130783718]N	.	.	SVTYPE=BND;STRANDS=-+:4;EVENT=3;MATEID=3_2;CIPOS=-10,9;CIEND=-10,9;CIPOS95=-1,1;CIEND95=-1,1;IMPRECISE;SU=4;PE=1;SR=3;PRPOS=8.23016e-13,1.31329e-11,2.09771e-10,3.347e-09,5.34553e-08,8.53258e-07,1.36259e-05,0.000217259,0.00346568,0.0551999,0.88134,0.0559631,0.00355855,0.00022594,1.4338e-05,9.08558e-07,5.7626e-08,3.65831e-09,9.18926e-11,2.30824e-12;PREND=9.82279e-13,1.54152e-11,2.41893e-10,3.77889e-09,5.93699e-08,9.25795e-07,1.45855e-05,0.000228742,0.00360339,0.0562406,0.881709,0.054589,0.00338949,0.000210056,1.31444e-05,8.21092e-07,5.1112e-08,3.18107e-09,1.97944e-10,1.23366e-11	GT:SU:PE:SR	./.:0:0:0	./.:4:1:3
+9	130783718	3_2	N	N[22:23292033[	.	.	SVTYPE=BND;STRANDS=+-:4;SECONDARY;EVENT=3;MATEID=3_1;CIPOS=-10,9;CIEND=-10,9;CIPOS95=-1,1;CIEND95=-1,1;IMPRECISE;SU=4;PE=1;SR=3;PRPOS=9.82279e-13,1.54152e-11,2.41893e-10,3.77889e-09,5.93699e-08,9.25795e-07,1.45855e-05,0.000228742,0.00360339,0.0562406,0.881709,0.054589,0.00338949,0.000210056,1.31444e-05,8.21092e-07,5.1112e-08,3.18107e-09,1.97944e-10,1.23366e-11;PREND=8.23016e-13,1.31329e-11,2.09771e-10,3.347e-09,5.34553e-08,8.53258e-07,1.36259e-05,0.000217259,0.00346568,0.0551999,0.88134,0.0559631,0.00355855,0.00022594,1.4338e-05,9.08558e-07,5.7626e-08,3.65831e-09,9.18926e-11,2.30824e-12	GT:SU:PE:SR	./.:0:0:0	./.:4:1:3
Binary file test-data/sample_Del.bam has changed
Binary file test-data/sample_cle.bam has changed