# HG changeset patch
# User iuc
# Date 1611172180 0
# Node ID 630e2929a13195635a931a97b8a06bcddda9f7f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
diff -r 000000000000 -r 630e2929a131 jasminesv.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jasminesv.xml Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,197 @@
+
+
+ Merge structural variants across samples
+
+ macros.xml
+
+
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+
+
+
+
+ #
+#for $vcf_file in $vcf_list:
+${vcf_file}
+#end for
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diff -r 000000000000 -r 630e2929a131 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,66 @@
+
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+ 1.0.11
+ 0
+ 20.01
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+ jasminesv
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+ jasmine
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+ @online{jasmine,
+ author = {Melanie Kirsche},
+ title = {jasmine},
+ year = 2021,
+ url = {https://github.com/mkirsche/Jasmine},
+ urldate = {2021-01-13}
+ }
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+ `_.
+ ]]>
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diff -r 000000000000 -r 630e2929a131 test-data/a.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/a.vcf Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,15 @@
+##fileformat=VCFv4.1
+##contig=
+##contig=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FORMAT=
+1 100 1 CACGTACGTACGTACGTACGTACGTACTGACGTACGT C . PASS PRECISE;CHR2=1;END=136;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-36;STRANDS=+-;RE=12;IS_SPECIFIC=1 GT 1/1
+1 200 2 C CACGTACGTACGTACGTACGTACGTACTGACGTACGT . PASS PRECISE;CHR2=1;END=200;SVTYPE=INS;SUPTYPE=AL;SVLEN=36;STRANDS=+-;RE=10;IS_SPECIFIC=1 GT 1/1
+1 300 3 N ]2:1000000]N . PASS PRECISE;CHR2=2;END=3000000;SVTYPE=BND;SUPTYPE=AL;SVLEN=1;STRANDS=-+;RE=15;IS_SPECIFIC=1 GT 1/1
diff -r 000000000000 -r 630e2929a131 test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,19 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
+jasmine jasmine jasmine ${__HERE__}/genome.fa
\ No newline at end of file
diff -r 000000000000 -r 630e2929a131 test-data/b.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b.vcf Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,15 @@
+##fileformat=VCFv4.1
+##contig=
+##contig=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FORMAT=
+1 100 1 CACGTACGTACGTACGTACGTACGTACTGACGT C . PASS PRECISE;CHR2=1;END=132;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-32;STRANDS=+-;RE=12;IS_SPECIFIC=1 GT 1/1
+1 205 2 C CACGTACGTACGTACGTACGTACGTACTGACGTACGTACGT . PASS PRECISE;CHR2=1;END=205;SVTYPE=INS;SUPTYPE=AL;SVLEN=40;STRANDS=+-;RE=10;IS_SPECIFIC=1 GT 1/1
+1 300 3 N ]2:1000000]N . PASS PRECISE;CHR2=2;END=3000000;SVTYPE=BND;SUPTYPE=AL;SVLEN=1;STRANDS=-+;RE=15;IS_SPECIFIC=1 GT 1/1
diff -r 000000000000 -r 630e2929a131 test-data/c.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/c.vcf Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,15 @@
+##fileformat=VCFv4.1
+##contig=
+##contig=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FORMAT=
+chr1 100 1 CACGTACGTACGTACGTACGTACGTACTGACGTACGT C . PASS PRECISE;CHR2=1;END=136;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-36;STRANDS=+-;RE=12;IS_SPECIFIC=1 GT 1/1
+chr1 200 2 C CACGTACGTACGTACGTACGTACGTACTGACGTACGT . PASS PRECISE;CHR2=1;END=200;SVTYPE=INS;SUPTYPE=AL;SVLEN=36;STRANDS=+-;RE=10;IS_SPECIFIC=1 GT 1/1
+chr1 300 3 N ]2:1000000]N . PASS PRECISE;CHR2=2;END=3000000;SVTYPE=BND;SUPTYPE=AL;SVLEN=1;STRANDS=-+;RE=15;IS_SPECIFIC=1 GT 1/1
diff -r 000000000000 -r 630e2929a131 test-data/chr_norm_file.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr_norm_file.txt Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,2 @@
+chr1 1
+chr2 2
diff -r 000000000000 -r 630e2929a131 test-data/d.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/d.vcf Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,15 @@
+##fileformat=VCFv4.1
+##contig=
+##contig=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FORMAT=
+chr1 100 1 CACGTACGTACGTACGTACGTACGTACTGACGT C . PASS PRECISE;CHR2=1;END=132;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-32;STRANDS=+-;RE=12;IS_SPECIFIC=1 GT 1/1
+chr1 205 2 C CACGTACGTACGTACGTACGTACGTACTGACGTACGTACGT . PASS PRECISE;CHR2=1;END=205;SVTYPE=INS;SUPTYPE=AL;SVLEN=40;STRANDS=+-;RE=10;IS_SPECIFIC=1 GT 1/1
+chr1 300 3 N ]2:1000000]N . PASS PRECISE;CHR2=2;END=3000000;SVTYPE=BND;SUPTYPE=AL;SVLEN=1;STRANDS=-+;RE=15;IS_SPECIFIC=1 GT 1/1
diff -r 000000000000 -r 630e2929a131 test-data/genome.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fa Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,20 @@
+>1
+TAACCCTAACACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC
+TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAA
+CACGTACGTACGTACGTACGTACGTACTGACGTACGT
+AACCCTAACCCAA
+CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAAC
+CCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCT
+CACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTAAACCC
+TAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCCAACCCCA
+ACCCCAACCCCAACCCTAACCCCTAACCCTAACCCTAACCCTACCCTAAC
+>2
+TAACCCTAACACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC
+TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAA
+CACGTACGTACGTACGTACGTACGTACTGACGTACGT
+AACCCTAACCCAA
+CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAAC
+CCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCT
+CACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTAAACCC
+TAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCCAACCCCA
+ACCCCAACCCCAACCCTAACCCCTAACCCTAACCCTAACCCTACCCTAAC
\ No newline at end of file
diff -r 000000000000 -r 630e2929a131 test-data/out1.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out1.vcf Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,27 @@
+##fileformat=VCFv4.1
+##contig=
+##contig=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FORMAT=
+1 100 0_1 CACGTACGTACGTACGTACGTACGTACTGACGTACGT C . PASS PRECISE;CHR2=1;END=136;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-36;STRANDS=+-;RE=12;IS_SPECIFIC=1;STARTVARIANCE=0.000000;ENDVARIANCE=4.000000;AVG_LEN=-34.000000;AVG_START=100.000000;AVG_END=134.000000;SUPP_VEC_EXT=11;IDLIST_EXT=1,1;SUPP_EXT=2;SUPP_VEC=11;SUPP=2;SVMETHOD=JASMINE;IDLIST=1,1 GT 1/1
+1 200 0_2 C CACGTACGTACGTACGTACGTACGTACTGACGTACGT . PASS PRECISE;CHR2=1;END=200;SVTYPE=INS;SUPTYPE=AL;SVLEN=36;STRANDS=+-;RE=10;IS_SPECIFIC=1;STARTVARIANCE=6.250000;ENDVARIANCE=6.250000;AVG_LEN=38.000000;AVG_START=202.500000;AVG_END=202.500000;SUPP_VEC_EXT=11;IDLIST_EXT=2,2;SUPP_EXT=2;SUPP_VEC=11;SUPP=2;SVMETHOD=JASMINE;IDLIST=2,2 GT 1/1
+1 300 0_3 N ]2:1000000]N . PASS PRECISE;CHR2=2;END=3000000;SVTYPE=BND;SUPTYPE=AL;SVLEN=1;STRANDS=-+;RE=15;IS_SPECIFIC=1;STARTVARIANCE=0.000000;ENDVARIANCE=0.000000;AVG_LEN=1.000000;AVG_START=300.000000;AVG_END=3000000.000000;SUPP_VEC_EXT=11;IDLIST_EXT=3,3;SUPP_EXT=2;SUPP_VEC=11;SUPP=2;SVMETHOD=JASMINE;IDLIST=3,3 GT 1/1
diff -r 000000000000 -r 630e2929a131 tool_data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data/all_fasta.loc.sample Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
\ No newline at end of file
diff -r 000000000000 -r 630e2929a131 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,7 @@
+
+
+
+ value, dbkey, name, path
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 630e2929a131 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,7 @@
+
+
+
+ value, dbkey, name, path
+
+
+
\ No newline at end of file