| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/merge_sites/1.0.1 (this tool) |
| merge_sites |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bowtie2 | 2.3.5 | package |
| samtools | 1.9 | package |
| bzip2 | 1.0.6 | package |
| snp-pipeline | 2.0.2 | 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 ./
#for $call in $calls
-n $call.element_identifier -f $call
#end for
-p "var.fit.vcf" > ./file
&& cfsan_snp_pipeline merge_sites -v 4 -n "var.fit.vcf" ./file ./filtered_snps -o $snplist
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
calls: list collection |
samples/sample1/var.flt_preserved.vcf samples/sample2/var.flt_preserved.vcf samples/sample3/var.flt_preserved.vcf samples/sample4/var.flt_preserved.vcf |