| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/filter_regions/1.0.1 (this tool) |
| filter_regions |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| samtools | 1.9 | package |
| bzip2 | 1.0.6 | package |
| snp-pipeline | 2.0.2 | package |
| boto3 | 1.9.134 | package |
| python | 3.6.8 | package |
| Additional information about this tool |
export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
mkdir -p ./samples/sample/ &&
cp $calls ./samples/sample/var.flt.vcf &&
echo "\$PWD/samples/sample" > ./alignment.txt &&
cfsan_snp_pipeline filter_regions ./alignment.txt $reference
&& cp ./samples/sample/var.flt_preserved.vcf $filcalls
&& cp ./samples/sample/var.flt_removed.vcf $excludes
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
reference: reference/lambda_virus.fasta calls: samples/sample1/var.flt.vcf |
attributes: name |
reference/lambda_virus.fasta samples/sample1/var.flt.vcf name |