# HG changeset patch # User iuc # Date 1673043044 0 # Node ID ef4b5ce71745256ae57e7516ee5cc453bf317451 planemo upload for repository https://github.com/bgruening/iuc/tree/master/tools/biscot commit cce7b9b092030d3bb23a706ca3bf2dece9c20b5f diff -r 000000000000 -r ef4b5ce71745 biscot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biscot.xml Fri Jan 06 22:10:44 2023 +0000 @@ -0,0 +1,131 @@ + + Bionano scaffolding correction + + macros.xml + + + + + + + + + +
+ + +
+ + + + + + + + log_file + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r ef4b5ce71745 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jan 06 22:10:44 2023 +0000 @@ -0,0 +1,17 @@ + + 2.3.3 + 0 + + + biscot + blat + ucsc-pslsort + ucsc-pslreps + + + + + 10.7717/peerj.10150 + + + diff -r 000000000000 -r ef4b5ce71745 test-data/bionano_key_file.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bionano_key_file.txt Fri Jan 06 22:10:44 2023 +0000 @@ -0,0 +1,3 @@ +CompntId CompntName CompntLength +1 Super_scaffold_3 4753350 +4 Super_scaffold_3 4753350 diff -r 000000000000 -r ef4b5ce71745 test-data/query_cmap_file.cmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/query_cmap_file.cmap Fri Jan 06 22:10:44 2023 +0000 @@ -0,0 +1,545 @@ +# hostname=6d61d934e61b +# $ cd /HybridScaffold; /RefAligner/amd2/RefAligner -o /data/jwd03f/main/053/913/53913897/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD -stdout -stderr -i /data/jwd03f/main/053/913/53913897/working/assignAlignType/assignAlignType_q.cmap -ref /data/jwd03f/main/053/913/53913897/working/align_final/step2.hybrid.cmap -maxmem 250 -maxthreads 24 -maxvirtmem 250 -RAmem 3 1 -res 2.9 -FP 0.6 -FN 0.06 -sf 0.20 -sd 0.0 -sr 0.01 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 6 -deltaY 6 -xmapchim 12 -hashgen 5 7 2.4 1.5 0.05 5.0 1 1 4 -hash -hashdelta 26 10 46 -hashMultiMatch 30 10 -insertThreads 24 -nosplit 2 -biaswt 0 -T 1e-10 -S -1000 -indel -PVres 2 -rres 0.9 -MaxSE 0.5 -HSDrange 1.0 -outlierBC -xmapUnique 14 -AlignRes 2. -outlierExtend 6 24 -Kmax 6 -resEstimate -BestRef 1 -f -mres 0.9 +# CompileDir= /home/users/sqa01/RefAlignerBuild/branches/12432.12463rel/12432.12463rel CompileCmd=/opt/gcc-9.3.0/bin/g++ -B/opt/binutils-2.34 -fopenmp -Ofast -march=znver2 -mavx2 -mfpmath=sse -DUSE_PFLOAT=1 -DUSE_RFLOAT=1 -DUSE_SSE=1 -DUSE_MFLOAT=1 -DUSE_EPOW=2 -I/home/users8/tanantharaman/sleef-081120/build/include -I/opt/glibc-2.31/include -DUSE_STATIC -freciprocal-math -fno-signed-zeros -fno-trapping-math -fno-tree-vectorize -mtune=znver2 -fno-lto-odr-type-merging -DRELEASE=1 -std=gnu++98 -Wl,--dynamic-linker=/opt/glibc-2.31/lib/ld-linux-x86-64.so.2 -Wl,--rpath=/opt/glibc-2.31/lib -Wl,--rpath=/opt/gcc-9.3.0/lib64 -lsleefinline -lrt -lmvec -L/home/users8/tanantharaman/sleef-081120/build/lib -L/opt/glibc-2.31/lib -L/opt/gcc-9.3.0/lib64 -static -static-libstdc++ -static-libgcc -s SVNversion=12463 $Header: http://svn.bnm.local:81/svn/Informatics/RefAligner/branches/12432/RefAligner.cpp 12458 2021-10-24 00:56:45Z tanantharaman $ +# FLAGS: USE_SSE=1 USE_AVX=1 USE_MIC=0 USE_PFLOAT=1 USE_RFLOAT=1 USE_MFLOAT=1 USE_EPOW=2 DEBUG=1 VERB=1 +# CMAP File Version: 0.1 +# Label Channels: 1 +# Nickase Recognition Site 1: gctcttc +# Number of Consensus Maps: 2 +# StdDev & Coverage refer to the interval between current site and next site +#h CMapId ContigLength NumSites SiteID LabelChannel Position StdDev Coverage Occurrence +#f int float 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715091.0 83 82 1 708941.2 141.9 98.3 98.3 +4 715091.0 83 83 1 715071.0 0.0 72.0 72.0 +4 715091.0 83 84 0 715091.0 0.0 0.0 0.0 diff -r 000000000000 -r ef4b5ce71745 test-data/reference_cmap_file.cmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference_cmap_file.cmap Fri Jan 06 22:10:44 2023 +0000 @@ -0,0 +1,636 @@ +# hostname=6d61d934e61b +# $ cd /HybridScaffold; /RefAligner/amd2/RefAligner -o /data/jwd03f/main/053/913/53913897/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD -stdout -stderr -i /data/jwd03f/main/053/913/53913897/working/assignAlignType/assignAlignType_q.cmap -ref /data/jwd03f/main/053/913/53913897/working/align_final/step2.hybrid.cmap -maxmem 250 -maxthreads 24 -maxvirtmem 250 -RAmem 3 1 -res 2.9 -FP 0.6 -FN 0.06 -sf 0.20 -sd 0.0 -sr 0.01 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 6 -deltaY 6 -xmapchim 12 -hashgen 5 7 2.4 1.5 0.05 5.0 1 1 4 -hash -hashdelta 26 10 46 -hashMultiMatch 30 10 -insertThreads 24 -nosplit 2 -biaswt 0 -T 1e-10 -S -1000 -indel -PVres 2 -rres 0.9 -MaxSE 0.5 -HSDrange 1.0 -outlierBC -xmapUnique 14 -AlignRes 2. -outlierExtend 6 24 -Kmax 6 -resEstimate -BestRef 1 -f -mres 0.9 +# CompileDir= /home/users/sqa01/RefAlignerBuild/branches/12432.12463rel/12432.12463rel CompileCmd=/opt/gcc-9.3.0/bin/g++ -B/opt/binutils-2.34 -fopenmp -Ofast -march=znver2 -mavx2 -mfpmath=sse -DUSE_PFLOAT=1 -DUSE_RFLOAT=1 -DUSE_SSE=1 -DUSE_MFLOAT=1 -DUSE_EPOW=2 -I/home/users8/tanantharaman/sleef-081120/build/include -I/opt/glibc-2.31/include -DUSE_STATIC -freciprocal-math -fno-signed-zeros -fno-trapping-math -fno-tree-vectorize -mtune=znver2 -fno-lto-odr-type-merging -DRELEASE=1 -std=gnu++98 -Wl,--dynamic-linker=/opt/glibc-2.31/lib/ld-linux-x86-64.so.2 -Wl,--rpath=/opt/glibc-2.31/lib -Wl,--rpath=/opt/gcc-9.3.0/lib64 -lsleefinline -lrt -lmvec -L/home/users8/tanantharaman/sleef-081120/build/lib -L/opt/glibc-2.31/lib -L/opt/gcc-9.3.0/lib64 -static -static-libstdc++ -static-libgcc -s SVNversion=12463 $Header: http://svn.bnm.local:81/svn/Informatics/RefAligner/branches/12432/RefAligner.cpp 12458 2021-10-24 00:56:45Z tanantharaman $ +# FLAGS: USE_SSE=1 USE_AVX=1 USE_MIC=0 USE_PFLOAT=1 USE_RFLOAT=1 USE_MFLOAT=1 USE_EPOW=2 DEBUG=1 VERB=1 +# CMAP File Version: 0.1 +# Label Channels: 1 +# Nickase Recognition Site 1: gctcttc +# Number of Consensus Maps: 1 +# StdDev refers to the interval between the current site and the next site +#h CMapId ContigLength NumSites SiteID LabelChannel Position StdDev Coverage Occurrence Mask +#f int float int int int float float float float Hex +1 4753350.0 624 1 1 4239.0 0.0 0.0 0.0 10 +1 4753350.0 624 2 1 17279.0 0.0 0.0 0.0 0 +1 4753350.0 624 3 1 19489.5 0.0 1.0 1.0 0 +1 4753350.0 624 4 1 37090.0 0.0 1.0 1.0 0 +1 4753350.0 624 5 1 55531.0 0.0 1.0 1.0 0 +1 4753350.0 624 6 1 58111.0 0.0 1.0 1.0 0 +1 4753350.0 624 7 1 93858.0 0.0 1.0 1.0 0 +1 4753350.0 624 8 1 97892.0 0.0 1.0 1.0 0 +1 4753350.0 624 9 1 105928.0 0.0 1.0 1.0 0 +1 4753350.0 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1970 +0000 +++ b/test-data/xml_configuration_file.xmap Fri Jan 06 22:10:44 2023 +0000 @@ -0,0 +1,12 @@ +# hostname=6d61d934e61b +# $ cd /HybridScaffold; /RefAligner/amd2/RefAligner -o /data/jwd03f/main/053/913/53913897/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD -stdout -stderr -i /data/jwd03f/main/053/913/53913897/working/assignAlignType/assignAlignType_q.cmap -ref /data/jwd03f/main/053/913/53913897/working/align_final/step2.hybrid.cmap -maxmem 250 -maxthreads 24 -maxvirtmem 250 -RAmem 3 1 -res 2.9 -FP 0.6 -FN 0.06 -sf 0.20 -sd 0.0 -sr 0.01 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 6 -deltaY 6 -xmapchim 12 -hashgen 5 7 2.4 1.5 0.05 5.0 1 1 4 -hash -hashdelta 26 10 46 -hashMultiMatch 30 10 -insertThreads 24 -nosplit 2 -biaswt 0 -T 1e-10 -S -1000 -indel -PVres 2 -rres 0.9 -MaxSE 0.5 -HSDrange 1.0 -outlierBC -xmapUnique 14 -AlignRes 2. -outlierExtend 6 24 -Kmax 6 -resEstimate -BestRef 1 -f -mres 0.9 +# CompileDir= /home/users/sqa01/RefAlignerBuild/branches/12432.12463rel/12432.12463rel CompileCmd=/opt/gcc-9.3.0/bin/g++ -B/opt/binutils-2.34 -fopenmp -Ofast -march=znver2 -mavx2 -mfpmath=sse -DUSE_PFLOAT=1 -DUSE_RFLOAT=1 -DUSE_SSE=1 -DUSE_MFLOAT=1 -DUSE_EPOW=2 -I/home/users8/tanantharaman/sleef-081120/build/include -I/opt/glibc-2.31/include -DUSE_STATIC -freciprocal-math -fno-signed-zeros -fno-trapping-math -fno-tree-vectorize -mtune=znver2 -fno-lto-odr-type-merging -DRELEASE=1 -std=gnu++98 -Wl,--dynamic-linker=/opt/glibc-2.31/lib/ld-linux-x86-64.so.2 -Wl,--rpath=/opt/glibc-2.31/lib -Wl,--rpath=/opt/gcc-9.3.0/lib64 -lsleefinline -lrt -lmvec -L/home/users8/tanantharaman/sleef-081120/build/lib -L/opt/glibc-2.31/lib -L/opt/gcc-9.3.0/lib64 -static -static-libstdc++ -static-libgcc -s SVNversion=12463 $Header: http://svn.bnm.local:81/svn/Informatics/RefAligner/branches/12432/RefAligner.cpp 12458 2021-10-24 00:56:45Z tanantharaman $ +# FLAGS: USE_SSE=1 USE_AVX=1 USE_MIC=0 USE_PFLOAT=1 USE_RFLOAT=1 USE_MFLOAT=1 USE_EPOW=2 DEBUG=1 VERB=1 +# XMAP File Version: 0.2 +# Label Channels: 1 +# Reference Maps From: /data/jwd03f/main/053/913/53913897/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_r.cmap +# Query Maps From: /data/jwd03f/main/053/913/53913897/working/align_final/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap +#h XmapEntryID QryContigID RefContigID QryStartPos QryEndPos RefStartPos RefEndPos Orientation Confidence HitEnum QryLen RefLen LabelChannel Alignment +#f int int int float float float float string float string float float int string +1 4 1 20.0 715071.0 19489.5 743436.5 + 92.15 7M1D12M1D8M1D2M1D9M1D4M1D10M1D1M1D23M1D2M1D5M 715091.0 4753350.0 1 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