| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_cnv/delly_cnv/0.9.1+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_cnv/delly_cnv/0.9.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/delly_cnv/delly_cnv/0.8.7+galaxy0 |
| delly_cnv |
| 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 |
ln -s '$input' 'input.bam' &&
ln -s '$input.metadata.bam_index' 'input.bam.bai' &&
ln -s '$generic.genome' genome.fa &&
ln -s '$generic.mappability' mappability.fa &&
## run
delly cnv
## generic options
--genome genome.fa
--quality '$generic.quality'
--mappability mappability.fa
--ploidy $generic.ploidy
--outfile 'result.bcf'
--covfile 'result.gz'
## cnv calling options
--sdrd $cnv.sdrd
--cn-offset $cnv.cnoffset
--cnv-size $cnv.cnvsize
#if $cnv.svfile
--svfile $cnv.svfile
#end if
#if $cnv.vcffile
--vcffile '$cnv.vcffile'
#end if
$cnv.segmentation
## read-depth window options
--window-size $read.windowsize
--window-offset $read.windowoffset
#if $read.bedintervals
--bed-intervals '$read.bedintervals'
#end if
--fraction-window $read.fractionwindow
$read.adaptivewindowing
## gc fragment normalization options
--scan-window $gc.scanwindow
--fraction-unique $gc.fractionunique
#if $gc.scanregions
--scan-regions '$gc.scanregions'
#end if
--mad-cutoff $gc.madcutoff
--percentile $gc.percentile
$gc.nowindowselection
## input
'input.bam'
## postprocessing
#if 'log' in $oo.out
|& tee '$out_log'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: normal.bam generic|genome: genome.fasta generic|mappability: map.fasta oo|out: ['cnv', 'coverage', 'log'] |
name: value name: value name: value |
normal.bam genome.fasta map.fasta value |
| Test-2 |
input: normal.bam generic|genome: genome.fasta generic|quality: 11 generic|mappability: map.fasta generic|ploidy: 3 cnv|sdrd: 3 cnv|cnoffset: 0.2 cnv|cnvsize: 1001 cnv|segmentation: True read|windowsize: 10001 read|windowoffset: 9999 read|fractionwindow: 0.24 read|adaptivewindowing: True gc|scanwindow: 10001 gc|fractionunique: 0.79 gc|madcutoff: 2 gc|percentile: 0.0006 gc|nowindowselection: True oo|out: ['cnv', 'coverage', 'log'] |
name: value name: value name: value |
normal.bam genome.fasta map.fasta value |