# HG changeset patch
# User iuc
# Date 1718400234 0
# Node ID 498748c8725244ce4019624fe460c6ae2b3d4d84
planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
diff -r 000000000000 -r 498748c87252 bam_bed_gff_to_bigwig.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_bed_gff_to_bigwig.xml Fri Jun 14 21:23:54 2024 +0000
@@ -0,0 +1,109 @@
+
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+ UCSC_Genome_Browser_Utilities
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+ ucsc-bedgraphtobigwig
+ bedtools
+ coreutils
+ python
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+
+
+
+ input2 &&
+#else:
+ ln -s '$input1' input2 &&
+#end if
+#if $input1.ext == "bam":
+ bedtools genomecov -bg -split -ibam input2 |
+#else
+ bedtools genomecov -bg -i input2 -g ./CHROMFILE |
+#end if
+LC_COLLATE=C sort -k1,1 -k2,2n > temp.bg &&
+bedGraphToBigWig temp.bg ./CHROMFILE '$output'
+ ]]>
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+ Estimates coverage of a reference genome for bam, bed or gff as a bigwig, suitable for viewing in JBrowse2 or other browser.
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+ A chromosome lengths file must be provided if the input has a missing dbkey='?' on the pencil (edit attributes) tab.
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+ The actual reference is not needed. The Compute sequence length tool can generate the lengths file.
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+ This can be useful in workflows with assemblies in progress before a stable reference is available for a custom or built in reference dbkey.
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+
+
+ 10.1093/bioinformatics/btq351
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+
diff -r 000000000000 -r 498748c87252 gff_to_bed_converter.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gff_to_bed_converter.py Fri Jun 14 21:23:54 2024 +0000
@@ -0,0 +1,33 @@
+#!/usr/bin/env python
+
+import sys
+
+assert sys.version_info[:2] >= (2, 6)
+
+
+def __main__():
+ skipped_lines = 0
+ first_skipped_line = None
+ # was sys.argv[2] but we need stdout for a pipe in bam_bed_gff_to_bigwig.xml
+ for i, line in enumerate(sys.stdin):
+ line = line.rstrip("\r\n")
+ if line and not line.startswith("#"):
+ try:
+ elems = line.split("\t")
+ start = str(int(elems[3]) - 1)
+ endoff = str(int(elems[4]) - 1)
+ # GFF format: chrom, source, name, chromStart, chromEnd, score, strand
+ # bedtools puts out only 4 fields: chrom, chromStart, chromEnd, score
+ sys.stdout.write(f"{elems[0]}\t{start}\t{endoff}\t0\n")
+ except Exception:
+ skipped_lines += 1
+ if not first_skipped_line:
+ first_skipped_line = i + 1
+ else:
+ skipped_lines += 1
+ if not first_skipped_line:
+ first_skipped_line = i + 1
+
+
+if __name__ == "__main__":
+ __main__()
diff -r 000000000000 -r 498748c87252 test-data/dbkeys.loc.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbkeys.loc.test Fri Jun 14 21:23:54 2024 +0000
@@ -0,0 +1,2 @@
+#
+hg38 hg38 ${__HERE__}/testing.len
diff -r 000000000000 -r 498748c87252 test-data/featureCounts_input1.bam
Binary file test-data/featureCounts_input1.bam has changed
diff -r 000000000000 -r 498748c87252 test-data/featureCounts_input1.bigwig
Binary file test-data/featureCounts_input1.bigwig has changed
diff -r 000000000000 -r 498748c87252 test-data/merlin.bed.bigwig
Binary file test-data/merlin.bed.bigwig has changed
diff -r 000000000000 -r 498748c87252 test-data/merlin.gff.bigwig
Binary file test-data/merlin.gff.bigwig has changed
diff -r 000000000000 -r 498748c87252 test-data/srma_out2.bam
Binary file test-data/srma_out2.bam has changed
diff -r 000000000000 -r 498748c87252 test-data/srma_out2.bigwig
Binary file test-data/srma_out2.bigwig has changed
diff -r 000000000000 -r 498748c87252 test-data/test-6.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-6.bed Fri Jun 14 21:23:54 2024 +0000
@@ -0,0 +1,3 @@
+Merlin 49 1452 chromosomal_replication_initiator_protein_DnaA 0 +
+Merlin 1457 2557 DNA_polymerase_III_subunit_beta 0 +
+Merlin 2557 3630 DNA_replication_and_repair_protein_RecF 0 +
diff -r 000000000000 -r 498748c87252 test-data/test5.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test5.bed Fri Jun 14 21:23:54 2024 +0000
@@ -0,0 +1,17 @@
+chr7 115444712 115444739 CCDS5763.1_cds_0_0_chr7_115444713_f 0 +
+chr7 115468538 115468624 CCDS5763.1_cds_1_0_chr7_115468539_f 0 +
+chr7 115483024 115483277 CCDS5763.1_cds_2_0_chr7_115483025_f 0 +
+chr7 115484165 115484501 CCDS5763.1_cds_3_0_chr7_115484166_f 0 +
+chr7 115485764 115485980 CCDS5763.1_cds_4_0_chr7_115485765_f 0 +
+chr7 115486322 115486481 CCDS5763.1_cds_5_0_chr7_115486323_f 0 +
+chr7 115491298 115491487 CCDS5763.1_cds_6_0_chr7_115491299_f 0 +
+chr7 115468538 115468624 CCDS5764.1_cds_0_0_chr7_115468539_f 0 +
+chr7 115483024 115483277 CCDS5764.1_cds_1_0_chr7_115483025_f 0 +
+chr7 115484165 115484501 CCDS5764.1_cds_2_0_chr7_115484166_f 0 +
+chr7 115485764 115485980 CCDS5764.1_cds_3_0_chr7_115485765_f 0 +
+chr7 115486322 115486481 CCDS5764.1_cds_4_0_chr7_115486323_f 0 +
+chr7 115491298 115491487 CCDS5764.1_cds_5_0_chr7_115491299_f 0 +
+chr7 115733786 115733936 CCDS5766.1_cds_0_0_chr7_115733787_f 0 +
+chr7 115734264 115734452 CCDS5766.1_cds_1_0_chr7_115734265_f 0 +
+chr7 115739975 115740126 CCDS5766.1_cds_2_0_chr7_115739976_f 0 +
+chr7 115733786 115733936 CCDS5765.1_cds_0_0_chr7_115733787_f 0 +
diff -r 000000000000 -r 498748c87252 test-data/test5.bed.bigwig
Binary file test-data/test5.bed.bigwig has changed
diff -r 000000000000 -r 498748c87252 test-data/test5.gff.bigwig
Binary file test-data/test5.gff.bigwig has changed
diff -r 000000000000 -r 498748c87252 test-data/test5.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test5.gff3 Fri Jun 14 21:23:54 2024 +0000
@@ -0,0 +1,38 @@
+##gff-version 3
+##date Tue Jun 26 10:48:17 2007
+##sequence-region ctgA 1 50000
+##source gbrowse GFFToGalaxyDumper plugin
+##NOTE: All features dumped.
+ctgA example my_feature 22132 24633 . + . ID=My_feature:f15
+ctgA example my_feature 46990 48410 . - . ID=My_feature:f11
+ctgA example my_feature 44705 47713 . - . ID=My_feature:f01
+ctgA example my_feature 36649 40440 . - . ID=My_feature:f03
+ctgA example my_feature 23072 23185 . + . ID=My_feature:f14
+ctgA example my_feature 37242 38653 . + . ID=My_feature:f04
+ctgA example motif 37497 40559 . - . ID=Motif:m15;Note=7-transmembrane
+ctgA example my_feature 36034 38167 . + . ID=My_feature:f09
+ctgA example motif 28332 30033 . - . ID=Motif:m02;Note=HOX
+ctgA example my_feature 4715 5968 . - . ID=My_feature:f05
+ctgA example motif 48253 48366 . + . ID=Motif:m01;Note=WD40
+ctgA example BAC 1000 20000 . . . ID=BAC:b101.2;Note=Fingerprinted+BAC+with+end+reads
+ctgA example right_end_read 19500 20000 . - . Parent=BAC:b101.2
+ctgA example left_end_read 1000 1500 . + . Parent=BAC:b101.2
+ctgA example motif 13801 14007 . - . ID=Motif:m05;Note=helix+loop+helix
+ctgA example coding 1050 9000 . + . ID=mRNA:EDEN.1;Gene=EDEN
+ctgA example CDS 1201 1500 . + 0 Parent=mRNA:EDEN.1
+ctgA example CDS 3000 3902 . + 0 Parent=mRNA:EDEN.1
+ctgA example CDS 5000 5500 . + 0 Parent=mRNA:EDEN.1
+ctgA example CDS 7000 7608 . + 0 Parent=mRNA:EDEN.1
+ctgA example processed_transcript 1050 9000 . + . ID=mRNA:EDEN.1
+ctgA example 5'-UTR 1050 1200 . + . Parent=mRNA:EDEN.1
+ctgA example 3'-UTR 7609 9000 . + . Parent=mRNA:EDEN.1
+ctgA est match 5410 7503 . - . ID=EST:agt830.3;Target=agt830.3+1+595
+ctgA est HSP 7000 7503 . - . Parent=EST:agt830.3;Target=agt830.3+1+504
+ctgA est HSP 5410 5500 . - . Parent=EST:agt830.3;Target=agt830.3+505+595
+ctgA example motif 46012 48851 . + . ID=Motif:m09;Note=kinase
+ctgA example match 6885 8999 . - . ID=Match:seg03
+ctgA example HSP 8306 8999 . - . Parent=Match:seg03
+ctgA example HSP 8055 8080 . - . Parent=Match:seg03
+ctgA example HSP 7410 7737 . - . Parent=Match:seg03
+ctgA example HSP 6885 7241 . - . Parent=Match:seg03
+ctgA example my_feature 13280 16394 . + . ID=My_feature:f08
diff -r 000000000000 -r 498748c87252 test-data/testing.len
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testing.len Fri Jun 14 21:23:54 2024 +0000
@@ -0,0 +1,30 @@
+dummy_chr 100000000
+chr1 1000000000
+X 1000000000
+16 1000000000
+ctgA 1000000000
+Merlin 10000000
+super_1 1000000000
+chr1 1000000000
+chr7 2000000000
+chrX 2000000000
+phiX174 100000000
+random_phiX_region_1 100000000
+random_phiX_region_2 100000000
+random_phiX_region_3 100000000
+random_phiX_region_4 100000000
+random_phiX_region_5 100000000
+random_phiX_region_6 100000000
+random_phiX_region_7 100000000
+random_phiX_region_8 100000000
+random_phiX_region_9 100000000
+random_phiX_region_10 100000000
+random_phiX_region_11 100000000
+random_phiX_region_12 100000000
+random_phiX_region_13 100000000
+random_phiX_region_14 100000000
+random_phiX_region_15 100000000
+random_phiX_region_16 100000000
+random_phiX_region_17 100000000
+random_phiX_region_18 100000000
+random_phiX_region_19 100000000
diff -r 000000000000 -r 498748c87252 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Jun 14 21:23:54 2024 +0000
@@ -0,0 +1,7 @@
+
+
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+ value, name, len_path
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 498748c87252 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Fri Jun 14 21:23:54 2024 +0000
@@ -0,0 +1,7 @@
+
+
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+ value, name, len_path
+
+
+