| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_filter/delly_filter/0.9.1+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_filter/delly_filter/0.9.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_filter/delly_filter/0.8.7+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_filter/delly_filter/0.8.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_filter/delly_filter/0.8.3+galaxy0 |
| delly_filter |
| 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
#if $input.is_of_type('vcf')
bcftools view -Ob '$input' > 'input.bcf.gz' &&
bcftools index 'input.bcf.gz' &&
#else
ln -s '${input}' 'input.bcf.gz' &&
ln -s '${input.metadata.bcf_index}' 'input.bcf.gz.csi' &&
#end if
## run
delly filter
## generic options
--filter $sv.mode_cond.mode_sel
--outfile 'result.bcf'
--altaf $generic.altaf
--minsize $generic.minsize
--maxsize $generic.maxsize
--ratiogeno $generic.ratiogeno
$generic.pass
## somatic options
#if $sv.mode_cond.mode_sel == 'somatic'
--samples '$sv.mode_cond.samples'
--coverage $sv.mode_cond.coverage
--controlcontamination $sv.mode_cond.controlcontamination
## germline options
#else if $sv.mode_cond.mode_sel == 'germline'
--gq $sv.mode_cond.gq
--rddel $sv.mode_cond.rddel
--rddup $sv.mode_cond.rddup
#end if
## input
'input.bcf.gz'
## 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 sv|mode_cond|samples: samples.tsv sv|mode_cond|mode_sel: somatic oo|out: ['vcf', 'bcf'] |
name: value name: value |
call_1.bcf.gz samples.tsv value |
| Test-2 |
input: call_1.bcf.gz generic|altaf: 0.3 generic|minsize: 1 generic|maxsize: 500000001 generic|ratiogeno: 0.76 generic|pass: True sv|mode_cond|samples: samples.tsv sv|mode_cond|coverage: 11 sv|mode_cond|controlcontamination: 0.1 sv|mode_cond|mode_sel: somatic oo|out: ['vcf', 'bcf', 'log'] |
name: value name: value name: value |
call_1.bcf.gz samples.tsv value |
| Test-3 |
input: call_1.bcf.gz sv|mode_cond|mode_sel: germline oo|out: ['vcf', 'bcf'] |
name: value name: value |
call_1.bcf.gz value |
| Test-4 |
input: call_1.bcf.gz generic|altaf: 0.1 generic|minsize: 1 generic|maxsize: 500000001 generic|ratiogeno: 0.76 generic|pass: True sv|mode_cond|gq: 14 sv|mode_cond|rddel: 0.7 sv|mode_cond|rddup: 1.3 sv|mode_cond|mode_sel: germline oo|out: ['vcf', 'bcf', 'log'] |
name: value name: value name: value |
call_1.bcf.gz value |
| Test-5 |
input: call_1.vcf.gz sv|mode_cond|samples: samples.tsv sv|mode_cond|mode_sel: somatic oo|out: ['vcf', 'bcf'] |
name: value name: value |
call_1.vcf.gz samples.tsv value |