| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_aggregate_plot/freyja_aggregate_plot/1.5.2+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_aggregate_plot/freyja_aggregate_plot/1.5.2+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_aggregate_plot/freyja_aggregate_plot/1.5.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_aggregate_plot/freyja_aggregate_plot/1.4.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/freyja_aggregate_plot/freyja_aggregate_plot/1.3.8+galaxy0 |
| freyja_aggregate_plot |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| freyja | 1.5.2 | package |
| Additional information about this tool |
#if $need_aggregation.choice == 'yes'
#set demix_dir = 'demix_outputs/'
#set file_paths1 = []
mkdir -p demix_outputs &&
#for $input_file in $demix_file
#set $file_path = $demix_dir + $input_file.element_identifier
ln -s '$input_file' '$file_path' &&
$file_paths1.append($file_path)
#end for
freyja aggregate
'$demix_dir'
--output aggregated.tsv
#if $plot_format.choice != 'none'
&&
#end if
#end if
#if $plot_format.choice == 'dash'
echo '${plot_format.plot_title}' > plot_title.txt &&
echo '${plot_format.plot_intro}' > plot_intro.txt &&
freyja dash
--mincov $plot_format.mincov
#if $need_aggregation.choice == 'no'
'$tsv_aggregated'
#else
'aggregated.tsv'
#end if
'$plot_format.csv_meta'
plot_title.txt
plot_intro.txt
--output abundances_dashboard.html
#else if $plot_format.choice == 'plot'
freyja plot
$plot_format.lineages
--mincov $plot_format.mincov
#if $need_aggregation.choice == 'no'
$tsv_aggregated
#else
aggregated.tsv
#end if
--output abundances_plot.pdf
#if $plot_format.need_metadata.choice == 'yes'
--times '${plot_format.need_metadata.csv_meta}'
#if $plot_format.need_metadata.interval == 'MS'
--interval MS
#else
--interval D
--windowsize 70
#end if
#end if
#else if $plot_format.choice == 'plot_and_dash'
echo '${plot_format.plot_title}' > plot_title.txt &&
echo '${plot_format.plot_intro}' > plot_intro.txt &&
freyja dash
--mincov $plot_format.mincov
#if $need_aggregation.choice == 'no'
'$tsv_aggregated'
#else
'aggregated.tsv'
#end if
'$plot_format.csv_meta'
plot_title.txt
plot_intro.txt
--output abundances_dashboard.html
&&
freyja plot
$plot_format.lineages
--mincov $plot_format.mincov
#if $need_aggregation.choice == 'no'
'$tsv_aggregated'
#else
'aggregated.tsv'
#end if
--output abundances_plot.pdf
#if $plot_format.csv_meta
--times '${plot_format.csv_meta}'
#end if
#if $plot_format.interval == 'MS'
--interval MS
#else
--interval D
--windowsize 70
#end if
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
need_aggregation|demix_file: ['abundances.tsv', 'abundances2.tsv', 'abundances3.tsv', 'abundances4.tsv'] need_aggregation|choice: yes plot_format|choice: none |
name: value |
abundances.tsv abundances2.tsv abundances3.tsv abundances4.tsv value |
| Test-2 |
need_aggregation|tsv_aggregated: bunch_of_files.tsv need_aggregation|choice: no plot_format|csv_meta: csv_sample_meta.csv plot_format|plot_title: This is title plot_format|plot_intro: Local WW Dashboard plot_format|mincov: 75 plot_format|choice: dash |
name: value |
bunch_of_files.tsv csv_sample_meta.csv value |
| Test-3 |
need_aggregation|tsv_aggregated: bunch_of_files.tsv need_aggregation|choice: no plot_format|need_metadata|csv_meta: times_metadata.csv plot_format|need_metadata|interval: D plot_format|need_metadata|choice: yes plot_format|lineages: True plot_format|choice: plot |
name: value |
bunch_of_files.tsv times_metadata.csv value |
| Test-4 |
need_aggregation|demix_file: ['abundances.tsv', 'abundances2.tsv', 'abundances3.tsv'] need_aggregation|choice: yes plot_format|csv_meta: csv_sample_meta2.csv plot_format|plot_title: Title plot_format|plot_intro: Dashboard plot_format|choice: dash |
name: value name: value |
abundances.tsv abundances2.tsv abundances3.tsv csv_sample_meta2.csv value |
| Test-5 |
need_aggregation|demix_file: ['abundances.tsv', 'abundances2.tsv', 'abundances3.tsv'] need_aggregation|choice: yes plot_format|need_metadata|csv_meta: csv_sample_meta2.csv plot_format|need_metadata|interval: D plot_format|need_metadata|choice: yes plot_format|choice: plot |
name: value name: value |
abundances.tsv abundances2.tsv abundances3.tsv csv_sample_meta2.csv value |
| Test-6 |
need_aggregation|demix_file: ['abundances.tsv', 'abundances2.tsv', 'abundances3.tsv'] need_aggregation|choice: yes plot_format|csv_meta: csv_sample_meta2.csv plot_format|plot_title: Title plot_format|plot_intro: Dashboard plot_format|interval: D plot_format|choice: plot_and_dash |
name: value name: value name: value |
abundances.tsv abundances2.tsv abundances3.tsv csv_sample_meta2.csv value |