| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_boot/freyja_boot/2.0.1+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_boot/freyja_boot/2.0.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_boot/freyja_boot/1.5.2+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_boot/freyja_boot/1.5.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_boot/freyja_boot/1.5.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_boot/freyja_boot/1.4.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_boot/freyja_boot/1.3.8+galaxy0 |
| freyja_boot |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| freyja | 2.0.1 | package |
| Additional information about this tool |
#if $usher_update_option.choice == 'update'
freyja update &&
#end if
ln -s '$variants_file' 'variants_file.vcf' &&
#if $usher_update_option.choice == 'custom'
ln -s '${usher_update_option.usher_barcodes}' usher_barcodes.csv &&
#end if
freyja boot
#if $variants_file.ext == 'vcf'
'variants_file.vcf'
#else
'$variants_file'
#end if
'$depth_file'
#if $eps
--eps '${eps}'
#end if
#if $meta
--meta '${meta}'
#end if
$confirmedonly
--pathogen '$pathogen'
--nt \${GALAXY_SLOTS:-4}
#if $nb
--nb $nb
#end if
--output_base 'boot_output'
#if $usher_update_option.choice == 'custom'
--barcodes usher_barcodes.csv
#end if
$boxplot_pdf
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
variants_file: variants.tsv depth_file: depths.tsv usher_update_option|choice: repo confirmedonly: False nb: 10 boxplot_pdf: True |
name: value name: value name: value name: value |
variants.tsv depths.tsv value |
| Test-2 |
variants_file: test.vcf depth_file: depths.tsv usher_update_option|choice: repo confirmedonly: False nb: 10 boxplot_pdf: False |
name: value name: value |
test.vcf depths.tsv value |
| Test-3 |
variants_file: variants.tsv depth_file: depths.tsv usher_update_option|usher_barcodes: usher_barcodes.csv usher_update_option|choice: custom confirmedonly: False nb: 10 boxplot_pdf: True |
name: value name: value name: value name: value |
variants.tsv depths.tsv usher_barcodes.csv value |