| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_genemetrics/cnvkit_genemetrics/0.9.12+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_genemetrics/cnvkit_genemetrics/0.9.11+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_genemetrics/cnvkit_genemetrics/0.9.11+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_genemetrics/cnvkit_genemetrics/0.9.10+galaxy0.1 |
| cnvkit_genemetrics |
| 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_filename_file' ./sample.cnr &&
#if $segment
ln -s '$segment' ./sample.cns &&
#end if
cnvkit.py genemetrics
./sample.cnr
--output gene_genemetrics.txt
#if $segment
--segment ./sample.cns
#end if
#if $threshold
--threshold $threshold
#end if
#if $min_probes
--min-probes $min_probes
#end if
$drop_low_coverage
$male_reference
#if str($Sample_sex.sex) == "yes":
#if '$Sample_sex.sample_sex' == "Male"
#set $sample_sex_val = "Male"
--sample-sex '$segment_method_val'
#else
--sample-sex '$Sample_sex.sample_sex'
#end if
#end if
$advanced_settings.mean
$advanced_settings.median
$advanced_settings.mode
$advanced_settings.ttest
$advanced_settings.stdev
$advanced_settings.sem
$advanced_settings.mad
$advanced_settings.mse
$advanced_settings.iqr
$advanced_settings.bivar
$advanced_settings.ci
$advanced_settings.pi
$advanced_settings.alpha
$advanced_settings.bootstrap
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_filename_file: sample.cnr min_probes: 3 threshold: 0.2 male_reference: True drop_low_coverage: True |
name: value |
sample.cnr value |