| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.4.4+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.4.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.3.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.1+galaxy0 |
| medaka_consensus_pipeline |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| medaka | 1.7.2 | package |
| Additional information about this tool |
## symlink seems insuffiencient (fai file is still created next to link target)
cp '$d' 'input_assembly.fa' &&
medaka_consensus
## optional
-m ${m}
-b $b
-o results
-t \${GALAXY_SLOTS:-4}
## required
-i '$i'
-d 'input_assembly.fa'
2>&1 | tee '$out_log'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
i: basecalls.fastq.gz d: assembly.fasta |
name: value name: value name: value |
basecalls.fastq.gz assembly.fasta value |
| Test-2 |
i: basecalls.fastq.gz d: assembly.fasta m: r941_min_fast_g303 b: 99 out: ['consensus', 'probs', 'calls', 'log', 'gaps'] |
name: value name: value name: value name: value name: value |
basecalls.fastq.gz assembly.fasta value |