| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_export_bed/cnvkit_export_bed/0.9.12+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_export_bed/cnvkit_export_bed/0.9.11+galaxy1 |
| cnvkit_export_bed |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| cnvkit | 0.9.12 | package |
| samtools | 1.21 | package |
| Additional information about this tool |
ln -s '$input_segmented_file' ./sample.cns &&
cnvkit.py export bed
./sample.cns
$advanced_settings.label_genes
#if $advanced_settings.sample_id
--sample-id '$advanced_settings.sample_id'
#end if
#if $advanced_settings.ploidy
--ploidy $advanced_settings.ploidy
#end if
#if str($advanced_settings.sample_sex) and $advanced_settings.sample_sex != ""
--sample-sex '$advanced_settings.sample_sex'
#end if
$advanced_settings.male_reference
--output sample.cnv.bed
#if $advanced_settings.diploid_parx_genome
--diploid-parx-genome '$advanced_settings.diploid_parx_genome'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_segmented_file: sample.cns advanced_settings|sample_id: SampleID advanced_settings|sample_sex: Female |
name: value |
sample.cns value |