Mercurial > repos > bgruening > hicup_truncater
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 |
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--- 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