| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_segment/cnvkit_segment/0.9.12+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_segment/cnvkit_segment/0.9.11+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_segment/cnvkit_segment/0.9.11+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_segment/cnvkit_segment/0.9.10+galaxy0.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_segment/cnvkit_segment/0.9.10+galaxy0 |
| cnvkit_segment |
| 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 '$filename' ./tumor.cnr &&
#if $additional_SNP_allelic_process.vcf
ln -s '$additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
#end if
#import os
cnvkit.py segment
./tumor.cnr
--output sample.cns
--processes \${GALAXY_SLOTS:-4}
#if $advanced_settings.dataframe
--dataframe '$advanced_settings.dataframe'
#end if
#if $advanced_settings.method == "cbs"
#set $method_val = "cbs"
--method '$method_val'
#else
--method '$advanced_settings.method'
#end if
#if str($advanced_settings.threshold)
--threshold $advanced_settings.threshold
#end if
$advanced_settings.drop_low_coverage
#if str($advanced_settings.drop_outliers)
--drop-outliers $advanced_settings.drop_outliers
#end if
$advanced_settings.smooth_cbs
#if $additional_SNP_allelic_process.vcf
--vcf ./vcf_file.vcf
#end if
#if $additional_SNP_allelic_process.sample_id
--sample-id '$additional_SNP_allelic_process.sample_id'
#end if
#if $additional_SNP_allelic_process.normal_id
--normal-id '$additional_SNP_allelic_process.normal_id'
#end if
#if str($additional_SNP_allelic_process.min_variant_depth)
--min-variant-depth $additional_SNP_allelic_process.min_variant_depth
#end if
#if str($additional_SNP_allelic_process.zygosity_freq)
--zygosity-freq $additional_SNP_allelic_process.zygosity_freq
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
filename: tumor.cnr advanced_settings|method: hmm advanced_settings|threshold: 2 advanced_settings|drop_low_coverage: True advanced_settings|drop_outliers: 2 |
name: value |
tumor.cnr value |