Get gene tree by Ensembl ID tool metadata

Miscellaneous

Name: Get gene tree by Ensembl ID

Description: using REST API

Id: get_genetree

Guid: toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_genetree/get_genetree/1.0.0

Version: 1.0.0

Version command string: None

Display in tool panel: True

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

toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_genetree/get_genetree/1.0.0 (this tool)

toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_genetree/get_genetree/0.1.2

toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_genetree/get_genetree/0.1.1

get_genetree

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

Requirements:

name

version

type

python

3.13

package

requests

2.32.3

package

Additional information about this tool

Command:

python3 '$__tool_directory__/get_genetree.py'
--id_type ${input_type_conditional.input_type}
#if $input_type_conditional.input_type == "gene_id"
    --species ${input_type_conditional.species}
#end if
-i '$input'
--format ${output_format.output_format_selector}
#if $output_format.output_format_selector == 'json'
    -s ${output_format.sequence.sequence_selector}
    #if $output_format.sequence.sequence_selector != 'none'
        -a ${output_format.sequence.aligned}
        -c ${output_format.sequence.cigar}
    #end if
#elif $output_format.output_format_selector == 'phyloxml'
    -s ${output_format.sequence.sequence_selector}
    #if $output_format.sequence.sequence_selector != 'none'
        -a ${output_format.sequence.aligned}
    #end if
#else
    --nh_format $output_format.nh_format
#end if
> '$output'

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

name: value

value

Test-2

input_type_conditional|species: Chicken
input_type_conditional|input_type: gene_id
input: ENSGALP00010009242
output_format|nh_format: simple
output_format|output_format_selector: nh

name: value

value

Test-3

name: value

value

Test-4

name: value

value