| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_merge/delly_merge/0.9.1+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_merge/delly_merge/0.9.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_merge/delly_merge/0.8.7+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_merge/delly_merge/0.8.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_merge/delly_merge/0.8.3+galaxy0 |
| delly_merge |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| delly | 0.9.1 | package |
| bcftools | 1.12 | package |
| Additional information about this tool |
## initialize
#for $i, $current in enumerate($input)
#if $current.is_of_type('vcf')
bcftools view -Ob '$current' > 'input_${i}.bcf.gz' &&
bcftools index 'input_${i}.bcf.gz' &&
#else
ln -s '${current}' 'input_${i}.bcf.gz' &&
ln -s '${current.metadata.bcf_index}' 'input_${i}.bcf.gz.csi' &&
#end if
#end for
## run
delly merge
## generic options
--outfile 'result.bcf'
--chunks $generic.chunks
--vaf $generic.vaf
--coverage $generic.coverage
--minsize $generic.minsize
--maxsize $generic.maxsize
$generic.cnvmode
$generic.precise
$generic.pass
## overlap options
--bp-offset $overlap.bpoffset
--rec-overlap $overlap.recoverlap
## input
#for $i, $current in enumerate($input)
'input_${i}.bcf.gz'
#end for
## postprocessing
#if 'log' in $oo.out
|& tee '$out_log'
#end if
#if 'vcf' in $oo.out
&& test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: ['call_1.bcf.gz', 'call_2.bcf.gz'] oo|out: ['vcf', 'bcf'] |
name: value name: value |
call_1.bcf.gz call_2.bcf.gz value |
| Test-2 |
input: ['call_1.bcf.gz', 'call_2.bcf.gz'] generic|chunks: 500 generic|vaf: 0.16 generic|coverage: 10 generic|minsize: 0 generic|maxsize: 1000000 generic|cnvmode: True generic|precise: True generic|pass: True oo|out: ['vcf', 'bcf', 'log'] |
name: value name: value name: value |
call_1.bcf.gz call_2.bcf.gz value |
| Test-3 |
input: ['call_1.vcf.gz', 'call_2.vcf.gz'] oo|out: ['vcf', 'bcf'] |
name: value name: value |
call_1.vcf.gz call_2.vcf.gz value |