| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_diagram/cnvkit_diagram/0.9.12+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_diagram/cnvkit_diagram/0.9.11+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_diagram/cnvkit_diagram/0.9.11+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_diagram/cnvkit_diagram/0.9.10+galaxy0.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_diagram/cnvkit_diagram/0.9.10+galaxy0 |
| cnvkit_diagram |
| 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_cnr_file' ./tumor.cnr &&
#if $advanced_settings.segment
ln -s '$advanced_settings.segment' ./segment.cns &&
#end if
cnvkit.py diagram
./tumor.cnr
--output sample-diagram.pdf
#if $advanced_settings.segment
--segment ./segment.cns
#end if
#if str($advanced_settings.threshold)
--threshold $advanced_settings.threshold
#end if
#if str($advanced_settings.min_probes)
--min-probes $advanced_settings.min_probes
#end if
$advanced_settings.male_reference
#if str($advanced_settings.Sample_sex.sex) == "yes":
#if '$advanced_settings.Sample_sex.sample_sex' == "Male"
#set $sample_sex_val = "Male"
--sample-sex '$segment_method_val'
#else
--sample-sex '$advanced_settings.Sample_sex.sample_sex'
#end if
#end if
$advanced_settings.no_shift_xy
#if $plot_aesthetics.title
--title '$plot_aesthetics.title'
#end if
#if $advanced_settings.chromosome
--chromosome '$advanced_settings.chromosome'
#end if
$plot_aesthetics.no_gene_labels
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_cnr_file: tumor.cnr advanced_settings|segment: sample.cns advanced_settings|threshold: 10 advanced_settings|male_reference: True |
name: value |
tumor.cnr sample.cns value |
| Test-2 |
input_cnr_file: tumor.cnr advanced_settings|segment: sample.cns advanced_settings|threshold: 10 advanced_settings|male_reference: True advanced_settings|Sample_sex|sex: yes |
name: value |
tumor.cnr sample.cns value |