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Repository revision

Revision: 4:d58cad5baa70

Repository 'data_manager_fetch_refseq'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/data_manager_fetch_refseq

RefSeq data manager tool metadata

Miscellaneous

Name: RefSeq data manager

Description: Fetch FASTA data from NCBI RefSeq and update all_fasta data table

Id: data_manager_fetch_refseq

Guid: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_fetch_refseq/data_manager_fetch_refseq/0.0.20

Version: 0.0.20

Version command string: None

Display in tool panel: False

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

toolshed.g2.bx.psu.edu/repos/iuc/data_manager_fetch_refseq/data_manager_fetch_refseq/0.0.20 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/data_manager_fetch_refseq/data_manager_fetch_refseq/0.0.19

toolshed.g2.bx.psu.edu/repos/iuc/data_manager_fetch_refseq/data_manager_fetch_refseq/0.0.18

data_manager_fetch_refseq

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

Requirements:

name

version

type

python

3.7

package

requests

2.22.0

package

Additional information about this tool

Command:

python '$__tool_directory__/fetch_refseq.py'
      #if str( $advanced.advanced_selector ) == 'advanced':
        ${advanced.compress}
      #end if
      --galaxy_datamanager_filename '${output_file}'
      --division_names ${division_names}
      --mol_types ${mol_types}
      #if str( $pin_date ) != 'NO':
        --pin_date '${pin_date}'
      #end if

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

division_names: plastid
mol_types: protein
advanced|advanced_selector: basic
pin_date: 2018-03-14

name: value

value

Test-2

division_names: plastid
mol_types: protein
advanced|compress: False
advanced|advanced_selector: advanced
pin_date: 2018-03-14

name: value

value