| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.27+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.23+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.22+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.22+galaxy@VERSION_SUFFIX@ |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.12 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.5+gx1 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.5 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.4.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.4 |
| toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.3 |
| minimap2 |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| minimap2 | 2.28 | package |
| samtools | 1.19.2 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
reference_source|ref_file: bwa-mem-mt-genome.fa reference_source|reference_source_selector: history fastq_input|fastq_input1: bwa-mem-fasta1.fa fastq_input|analysis_type_selector: sr fastq_input|fastq_input_selector: single |
name: value |
bwa-mem-mt-genome.fa bwa-mem-fasta1.fa value |
| Test-2 |
reference_source|ref_file: bwa-mem-mt-genome.fa reference_source|reference_source_selector: history fastq_input|fastq_input1: bwa-mem-fasta1.fa fastq_input|analysis_type_selector: sr fastq_input|fastq_input_selector: single io_options|output_format: CRAM |
name: value |
bwa-mem-mt-genome.fa bwa-mem-fasta1.fa value |
| Test-3 |
reference_source|ref_file: bwa-mem-mt-genome.fa reference_source|reference_source_selector: history fastq_input|fastq_input1: bwa-mem-fastq1.fq fastq_input|fastq_input2: bwa-mem-fastq2.fq fastq_input|fastq_input_selector: paired |
name: value |
bwa-mem-mt-genome.fa bwa-mem-fastq1.fq bwa-mem-fastq2.fq value |
| Test-4 |
reference_source|ref_file: bwa-mem-mt-genome.fa reference_source|reference_source_selector: history fastq_input|fastq_input1: bwa-mem-fastq1.fq.gz fastq_input|fastq_input2: bwa-mem-fastq2.fq fastq_input|fastq_input_selector: paired |
name: value |
bwa-mem-mt-genome.fa bwa-mem-fastq1.fq.gz bwa-mem-fastq2.fq value |
| Test-5 |
reference_source|ref_file: bwa-mem-mt-genome.fa reference_source|reference_source_selector: history fastq_input|fastq_input1: paired collection fastq_input|fastq_input_selector: paired_collection |
name: value |
bwa-mem-mt-genome.fa bwa-mem-fastq1.fq bwa-mem-fastq2.fq value |
| Test-6 |
reference_source|ref_file: bwa-mem-mt-genome reference_source|reference_source_selector: cached fastq_input|fastq_input1: bwa-mem-fasta1.fa fastq_input|analysis_type_selector: sr fastq_input|fastq_input_selector: single |
name: value |
bwa-mem-fasta1.fa value |
| Test-7 |
reference_source|ref_file: bwa-mem-mt-genome reference_source|reference_source_selector: cached fastq_input|fastq_input1: bwa-mem-fasta1.fa fastq_input|analysis_type_selector: sr fastq_input|fastq_input_selector: single mapping_options|min_occ_floor: 1000 alignment_options|A: 2 alignment_options|B: 8 alignment_options|O: 12 alignment_options|O2: 32 alignment_options|E: 2 alignment_options|E2: 1 alignment_options|z: 400 alignment_options|s: 40 io_options|cs: none |
name: value |
bwa-mem-fasta1.fa value |
| Test-8 |
reference_source|ref_file: mini_reads.fq reference_source|reference_source_selector: history fastq_input|fastq_input1: mini_reads.fq fastq_input|analysis_type_selector: ava-ont fastq_input|fastq_input_selector: single io_options|output_format: paf |
name: value |
mini_reads.fq value |
| Test-9 |
reference_source|ref_file: minimap2-self-homology.fasta reference_source|reference_source_selector: history fastq_input|fastq_input1: minimap2-self-homology.fasta fastq_input|analysis_type_selector: self-homology fastq_input|fastq_input_selector: single |
name: value |
minimap2-self-homology.fasta value |
| Test-10 |
reference_source|ref_file: bwa-mem-mt-genome.fa reference_source|reference_source_selector: history fastq_input|fastq_input1: bwa-mem-fasta1.fa fastq_input|analysis_type_selector: sr fastq_input|fastq_input_selector: single mapping_options|mask_len: 100 |
name: value |
bwa-mem-mt-genome.fa bwa-mem-fasta1.fa value |
| Test-11 |
reference_source|ref_file: pacbio_hifi_assembly.fa.gz reference_source|reference_source_selector: history fastq_input|fastq_input1: pacbio_hifi_reads.fasta.gz fastq_input|analysis_type_selector: map-hifi fastq_input|fastq_input_selector: single |
name: value |
pacbio_hifi_assembly.fa.gz pacbio_hifi_reads.fasta.gz value |
| Test-12 |
reference_source|ref_file: pacbio_hifi_assembly.fa reference_source|reference_source_selector: history fastq_input|fastq_input1: pacbio_hifi_reads.fasta.gz fastq_input|analysis_type_selector: map-hifi fastq_input|fastq_input_selector: single |
name: value |
pacbio_hifi_assembly.fa pacbio_hifi_reads.fasta.gz value |
| Test-13 |
reference_source|ref_file: bwa-mem-mt-genome.fa reference_source|reference_source_selector: history fastq_input|fastq_input1: bwa-mem-fasta1.fa fastq_input|analysis_type_selector: sr fastq_input|fastq_input_selector: single mapping_options|kmer_ocurrence_interval|lower_limit: 10 mapping_options|kmer_ocurrence_interval|upper_limit: 30 mapping_options|kmer_ocurrence_interval|interval: enabled |
name: value |
bwa-mem-mt-genome.fa bwa-mem-fasta1.fa value |