Mercurial > repos > bgruening > confab
changeset 5:119b462f0f69 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit ed9b6859de648aa5f7cde483732f5df20aaff90e
| author | bgruening |
|---|---|
| date | Tue, 07 May 2019 13:33:12 -0400 |
| parents | 4c4e812a67a2 |
| children | 461f64330945 |
| files | confab.xml |
| diffstat | 1 files changed, 8 insertions(+), 7 deletions(-) [+] |
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--- a/confab.xml Sat May 20 08:31:56 2017 -0400 +++ b/confab.xml Tue May 07 13:33:12 2019 -0400 @@ -13,6 +13,7 @@ -i ${infile.ext} -o sdf --confab + --verbose --rcutoff $RMSD --ecutoff $energy --conf $conformers @@ -21,12 +22,12 @@ ]]> </command> <inputs> - <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/> - <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' /> - <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' /> - <param name='conformers' type='integer' value='100' label='Max number of conformers to test' /> + <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates in SDF or MOL2 format" help="Dataset missing? See TIP below"/> + <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (Å)' help='Minimum RMSD deviation from the original conformation in order to be classified as a separate conformer.'/> + <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' help='Minimum energy difference to the original conformation in order to be classified as a separate conformer.'/> + <param name='conformers' type='integer' value='1000000' label='Max number of conformers to test' /> <param name='first_conformer' type='boolean' truevalue='--original' falsevalue='' - label='Include the input conformation as the first conformer' /> + label='Include the input conformation as the first conformer' help='If yes, the original conformation is included in the output file'/> </inputs> <outputs> <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/> @@ -48,9 +49,9 @@ **What this tool does** -Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialisation steps, is used to generate multiple conformers which are filtered on-the-fly to identify diverse low energy conformers. +Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialization steps, is used to generate multiple conformers, which are filtered on-the-fly to identify diverse low-energy conformers. -.. _Confab: https://code.google.com/p/confab/ +.. _Confab: https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html#confab -----