{"aliases":[],"author":"Andrey Kartashov","checker_url":"","contains":[],"description":"Usage:   bwa aln [options] <prefix> <in.fq>\n\nOptions: -n NUM    max #diff (int) or missing prob under 0.02 err rate (float) [0.04]\n         -o INT    maximum number or fraction of gap opens [1]\n         -e INT    maximum number of gap extensions, -1 for disabling long gaps [-1]\n         -i INT    do not put an indel within INT bp towards the ends [5]\n         -d INT    maximum occurrences for extending a long deletion [10]\n         -l INT    seed length [32]\n         -k INT    maximum differences in the seed [2]\n         -m INT    maximum entries in the queue [2000000]\n         -t INT    number of threads [1]\n         -M INT    mismatch penalty [3]\n         -O INT    gap open penalty [11]\n         -E INT    gap extension penalty [4]\n         -R INT    stop searching when there are >INT equally best hits [30]\n         -q INT    quality threshold for read trimming down to 35bp [0]\n         -f FILE   file to write output to instead of stdout\n         -B INT    length of barcode\n         -c        input sequences are in the color space\n         -L        log-scaled gap penalty for long deletions\n         -N        non-iterative mode: search for all n-difference hits (slooow)\n         -I        the input is in the Illumina 1.3+ FASTQ-like format\n         -b        the input read file is in the BAM format\n         -0        use single-end reads only (effective with -b)\n         -1        use the 1st read in a pair (effective with -b)\n         -2        use the 2nd read in a pair (effective with -b)\n","has_checker":false,"id":"quay.io/collaboratory/dockstore-tool-bwa-aln","meta_version":"2018-09-13 16:01:06.861","organization":"collaboratory","signed":false,"toolclass":{"description":"CommandLineTool","id":"0","name":"CommandLineTool"},"toolname":"dockstore-tool-bwa-aln","url":"https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fcollaboratory%2Fdockstore-tool-bwa-aln","verified":false,"verified_source":"[]","versions":[{"containerfile":true,"descriptor_type":["CWL"],"id":"quay.io/collaboratory/dockstore-tool-bwa-aln:1.0","image":"","image_name":"quay.io/collaboratory/dockstore-tool-bwa-aln","meta_version":"2016-09-14 20:31:51.0","name":"1.0","registry_url":"quay.io","url":"https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fcollaboratory%2Fdockstore-tool-bwa-aln/versions/1.0","verified":false,"verified_source":"[]"},{"containerfile":true,"descriptor_type":["CWL"],"id":"quay.io/collaboratory/dockstore-tool-bwa-aln:latest","image":"","image_name":"quay.io/collaboratory/dockstore-tool-bwa-aln","meta_version":"2016-09-15 12:49:34.0","name":"latest","registry_url":"quay.io","url":"https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fcollaboratory%2Fdockstore-tool-bwa-aln/versions/latest","verified":false,"verified_source":"[]"},{"containerfile":true,"descriptor_type":["CWL"],"id":"quay.io/collaboratory/dockstore-tool-bwa-aln:master","image":"","image_name":"quay.io/collaboratory/dockstore-tool-bwa-aln","meta_version":"2016-09-15 12:49:32.0","name":"master","registry_url":"quay.io","url":"https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fcollaboratory%2Fdockstore-tool-bwa-aln/versions/master","verified":false,"verified_source":"[]"}]}