Galaxy |

Krona pie chart tool metadata

Miscellaneous

Name: Krona pie chart

Description: from taxonomic profile

Id: taxonomy_krona_chart

Guid: toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0

Version: 2.7.1+galaxy0

Version command string: ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1

toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1

toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1

toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.0

toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.0.0

toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/1.0.0

taxonomy_krona_chart

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

krona

2.7.1

package

Additional information about this tool

Command:

#import re

    #if $type_of_data.input[0].is_of_type('taxonomy'):
        ktImportGalaxy
        -d '${type_of_data.max_rank}'
    #else:
        ktImportText
    #end if

    -n '${root_name}'
    -o '${output}'
    ${combine_inputs}
    #for $input_dataset in $type_of_data.input:
        #set $identifier=re.sub('[^\w\-\s]', '_', str($input_dataset.element_identifier))
        '${input_dataset},${identifier}'
    #end for
    &&
    if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

type_of_data|input: taxonomy_data.tax
type_of_data|max_rank: 18
type_of_data|type_of_data_selector: taxonomy
root_name: Root
combine_inputs: False

name: value

taxonomy_data.tax
value

Test-2

type_of_data|input: ['taxonomy_data.tax', 'tax2.tax']
type_of_data|max_rank: 18
type_of_data|type_of_data_selector: taxonomy
root_name: Root
combine_inputs: False

name: value

taxonomy_data.tax
tax2.tax
value

Test-3

type_of_data|input: ['pampa-small.tsv', 'anguil-small.tsv']
type_of_data|type_of_data_selector: text
root_name: Root
combine_inputs: False

name: value

pampa-small.tsv
anguil-small.tsv
value