diff test-data/dataset1_2.filt.sam @ 7:cc413be789ea draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17
author bgruening
date Thu, 23 Feb 2023 18:02:58 +0000
parents 30b199ed897d
children
line wrap: on
line diff
--- a/test-data/dataset1_2.filt.sam	Mon Oct 24 16:11:12 2022 +0000
+++ b/test-data/dataset1_2.filt.sam	Thu Feb 23 18:02:58 2023 +0000
@@ -1,13 +1,14 @@
-@HD	VN:1.5	SO:queryname
+@HD	VN:1.5	SO:unsorted	GO:query
 @SQ	SN:chr21	LN:46709983
 @SQ	SN:chr22	LN:50818468
-@PG	ID:bowtie2	PN:bowtie2	VN:2.4.5	CL:"/home/ldelisle/miniconda3/envs/__hicup@0.8.3/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome --threads 1 --reorder - --passthrough"
-@PG	ID:HiCUP Mapper	VN:0.8.3
-@PG	ID:samtools	PN:samtools	PP:HiCUP Mapper	VN:1.16.1	CL:samtools view -bSh -
-@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.15.1 (pysam)	CL:samtools sort -n -@1 -T /tmp/tmpqwp310ym/sorted -O BAM -o /tmp/tmpqwp310ym/sorted.bam /tmp/tmprolrrufe/job_working_directory/000/1/outputs/galaxy_dataset_2f0aefeb-faca-49dc-a585-09a611400a5e.dat
-@PG	ID:samtools.2	PN:samtools	PP:samtools.1	VN:1.16.1	CL:/home/ldelisle/miniconda3/envs/__hicup@0.8.3/bin/samtools view -h ./0.bam
-@PG	ID:HiCUP Filter	VN:0.8.3	DS:"Max insert 0 Min insert 0 Digest file /tmp/tmprolrrufe/files/c/8/e/dataset_c8ea51e8-38b0-4467-b22b-1b5878b2ab5f.dat"
-@PG	ID:samtools.3	PN:samtools	PP:samtools.2	VN:1.16.1	CL:samtools view -bSh -
+@PG	ID:bowtie2	PN:bowtie2	VN:2.4.5	CL:"/home/ldelisle/miniconda3/envs/mulled-v1-5c1994247e0ff8cda611e273476d9ea98cc0e3e62bd124f468f1ea5f3d75bca4/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome --threads 1 --reorder - --passthrough"
+@PG	ID:HiCUP Mapper	VN:0.9.2
+@PG	ID:HiCUP Truncater	VN:0.9.2	DS:"Restriction enzyme re1_unspecified [A^AGCTT]"
+@PG	ID:samtools	PN:samtools	PP:HiCUP Truncater	VN:1.16.1	CL:samtools view -bSh -
+@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.16.1	CL:/home/ldelisle/miniconda3/envs/mulled-v1-5c1994247e0ff8cda611e273476d9ea98cc0e3e62bd124f468f1ea5f3d75bca4/bin/samtools view -h dataset1_2.pair.bam
+@PG	ID:HiCUP Filter	VN:0.9.2	DS:"Max insert 0 Min insert 0 Digest file digest_file.txt"
+@PG	ID:samtools.2	PN:samtools	PP:samtools.1	VN:1.16.1	CL:samtools view -bSh -
+@PG	ID:samtools.3	PN:samtools	PP:samtools.2	VN:1.16.1	CL:samtools view -h dataset1_2.filt.bam
 SRR071233.29547	115	chr22	31119191	42	40M	=	28742824	0	GCCTCTAACCTACATGGCTCTGCTGCTTGAGATCCCCTCG	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC8CCCCCCCCC	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:40	YT:Z:UU	CT:Z:FAR
 SRR071233.29547	179	chr22	28742824	42	40M	=	31119191	0	TGGGCGAGGCCTGAGGGAAAAGTGAGAATTGGAGGGAGAG	CDCDBCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:40	YT:Z:UU	CT:Z:FAR
 SRR071233.80581	99	chr21	27660196	42	40M	=	15297495	0	TGCATATTCACTAACCGGGACAGTTAAAAATTAATATATT	CCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCC	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:40	YT:Z:UU	CT:Z:FAR