| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_fix/cnvkit_fix/0.9.12+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_fix/cnvkit_fix/0.9.11+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_fix/cnvkit_fix/0.9.11+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_fix/cnvkit_fix/0.9.10+galaxy0.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_fix/cnvkit_fix/0.9.10+galaxy0 |
| cnvkit_fix |
| 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_target_file' ./tumor.targetcoverage.cnn &&
#if $input_antitarget_file
ln -s '$input_antitarget_file' ./tumor.antitargetcoverage.cnn &&
#end if
#if $input_reference_coverage_file
ln -s '$input_reference_coverage_file' ./ref-tas.cnn &&
#end if
cnvkit.py fix
./tumor.targetcoverage.cnn
#if $input_antitarget_file
./tumor.antitargetcoverage.cnn
#end if
#if $input_reference_coverage_file
./ref-tas.cnn
#end if
--output sample.cnr
$cluster
#if $sample_id
--sample-id '$sample_id'
#end if
$no_gc
$no_edge
$no_rmask
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_target_file: tumor.targetcoverage.cnn input_antitarget_file: tumor.antitargetcoverage.cnn input_reference_coverage_file: ref-tas.cnn no_edge: True |
name: value |
tumor.targetcoverage.cnn tumor.antitargetcoverage.cnn ref-tas.cnn value |