| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_demix/freyja_demix/1.5.2+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_demix/freyja_demix/1.5.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_demix/freyja_demix/1.5.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_demix/freyja_demix/1.4.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_demix/freyja_demix/1.3.8+galaxy0 |
| freyja_demix |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| freyja | 1.5.2 | package |
| sed | 4.7 | package |
| Additional information about this tool |
#if $usher_update_option.choice == 'update'
freyja update &&
#end if
#if str($sample_name.source) == 'auto':
#set $sn = $variants_in.element_identifier
#else:
#set $sn = str($sample_name.name)
#end if
#if $usher_update_option.choice == 'custom'
ln -s '${usher_update_option.usher_barcodes}' usher_barcodes.csv &&
#end if
#set $in_file = $sn.replace(' ', '_') + '.' + $variants_in.ext
ln -s '$variants_in' $in_file &&
freyja demix
'$in_file'
'$depth_file'
#if $eps
--eps $eps
#end if
#if $meta
--meta '$meta'
#end if
$confirmedonly
$wgisaid
#if $usher_update_option.choice == 'custom'
--barcodes usher_barcodes.csv
#end if
--covcut $depth_cutoff
--output abundances_raw.tsv &&
sed 's/$in_file/$sn/' abundances_raw.tsv > abundances.tsv
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
variants_in: variants.tsv sample_name|name: samplename sample_name|source: manual depth_file: depths.tsv usher_update_option|choice: repo |
name: value |
variants.tsv depths.tsv value |
| Test-2 |
variants_in: variants.tsv sample_name|source: auto depth_file: depths.tsv usher_update_option|choice: repo |
name: value |
variants.tsv depths.tsv value |
| Test-3 |
variants_in: variants.tsv sample_name|source: auto depth_file: depths.tsv usher_update_option|usher_barcodes: usher_barcodes.csv usher_update_option|choice: custom |
name: value |
variants.tsv depths.tsv usher_barcodes.csv value |