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Prepare ligands for docking tool metadata

Miscellaneous

Name: Prepare ligands for docking

Description: Tool to prepare ligands for docking with tools like Autodock Vina

Id: prepare_ligands_for_docking

Guid: toolshed.g2.bx.psu.edu/repos/bgruening/prepare_ligands_for_docking/prepare_ligands_for_docking/3.1.1+galaxy0

Version: 3.1.1+galaxy0

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/bgruening/prepare_ligands_for_docking/prepare_ligands_for_docking/3.1.1+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/bgruening/prepare_ligands_for_docking/prepare_ligands_for_docking/2.4.2.2.0

toolshed.g2.bx.psu.edu/repos/bgruening/prepare_ligands_for_docking/prepare_ligands_for_docking/2.4.2.1.0

toolshed.g2.bx.psu.edu/repos/bgruening/prepare_ligands_for_docking/prepare_ligands_for_docking/2.4.2.0

prepare_ligands_for_docking

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

Requirements:

name

version

type

openbabel

3.1.1

package

python

3.6

package

Additional information about this tool

Command:

mkdir output && obabel -i '${ligands.ext}' -o '$oformat' -O 'output/molecule.$oformat' -m '$ligands' $gen3d -p $ph_value

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

ligands: ob_prepare_ligands.sdf
ph_value: 7.4
oformat: pdbqt

ob_prepare_ligands.sdf

Test-2

ligands: ob_prepare_ligands.sdf
ph_value: 7.4
oformat: mol2

ob_prepare_ligands.sdf

Test-3

ligands: ob_prepare_ligands.sdf
ph_value: 7.4
oformat: mol

ob_prepare_ligands.sdf

Test-4

ligands: ob_prepare_ligands.sdf
ph_value: 7.4
oformat: pdb

ob_prepare_ligands.sdf