| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/snp_matrix/1.0.1 (this tool) |
| snp_matrix |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bcftools | 1.9 | package |
| bzip2 | 1.0.6 | package |
| snp-pipeline | 2.0.2 | package |
| tabix | 0.2.5 | package |
| python | 3.6.8 | package |
| Additional information about this tool |
export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"
#for $fa in sorted($cons, key=lambda f: f.element_identifier)
-n $fa.element_identifier -f $fa
#end for
> ./file &&
cat ./file &&
cfsan_snp_pipeline snp_matrix -o $snpma ./file &&
cfsan_snp_pipeline distance -p $pairws -m $distma $snpma &&
cfsan_snp_pipeline snp_reference -l $snplist -o $referenceSNP $reference
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
reference|ref: history snplist: snplist.txt reference|reference: reference/lambda_virus.fasta cons: list collection |
attributes: name attributes: name attributes: name attributes: name |
samples/sample1/consensus.fasta samples/sample2/consensus.fasta samples/sample3/consensus.fasta samples/sample4/consensus.fasta reference/lambda_virus.fasta snplist.txt name |