Mercurial > repos > bgruening > openbabel_filter
changeset 7:91608f6db4e1 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
| author | bgruening |
|---|---|
| date | Tue, 07 May 2019 13:22:15 -0400 |
| parents | 336554b0d77e |
| children | 3f7bd33ee799 |
| files | macros.xml ob_filter.xml test-data/2_mol.dat test-data/CO.smarts |
| diffstat | 4 files changed, 26 insertions(+), 25 deletions(-) [+] |
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--- a/macros.xml Mon Sep 03 16:36:45 2018 -0400 +++ b/macros.xml Tue May 07 13:22:15 2019 -0400 @@ -1,9 +1,10 @@ <macros> - <token name="@VERSION@">2.4.1</token> + <token name="@VERSION@">2.4.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.4.1">openbabel</requirement> + <requirement type="package" version="3">python</requirement> <yield /> </requirements> </xml> @@ -37,6 +38,3 @@ </citations> </xml> </macros> - - -
--- a/ob_filter.xml Mon Sep 03 16:36:45 2018 -0400 +++ b/ob_filter.xml Tue May 07 13:22:15 2019 -0400 @@ -45,7 +45,7 @@ </command> <inputs> <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" - label="Select input file previously annotated with the 'Compute physico-chemical properties' tool"/> + label="Select input file (can be previously annotated with the 'Compute physico-chemical properties' tool)"/> <conditional name="filter_methods"> <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set"> <option value="user">User-defined properties</option> @@ -59,16 +59,16 @@ <when value="DrugLike" /> <when value="FragmentLike" /> <when value="user"> - <repeat name="filter_set" title="Filters selection"> + <repeat name="filter_set" title="Select custom filters"> <conditional name="filter_sel"> <param name="filter_sel_opts" type="select" label="Select properties to filter"> - <option value="hbd">Number of Hydrogen-bond donor groups</option> - <option value="hba">Number of Hydrogen-bond acceptor groups</option> - <option value="psa">Total polar Surface Area</option> + <option value="hbd">Number of hydrogen-bond donor groups</option> + <option value="hba">Number of hydrogen-bond acceptor groups</option> + <option value="psa">Total polar surface area</option> <option value="rotbonds">Number of rotatable bonds</option> <option value="molwt">Molecular weight</option> - <option value="logp">Predicted value of LogP</option> - <option value="mr">Predicted value for the Molecular Refractivity</option> + <option value="logp">Predicted value of logP</option> + <option value="mr">Predicted value for the molecular refractivity</option> <option value="atoms">Number of atoms</option> <!-- Add later, we need to add a new smarts pattern to plugindefines.txt <option value="hatoms">Number of heavy atoms</option>--> @@ -76,32 +76,32 @@ <!--<option value="rings">Number of rings</option>--> </param> <when value="hbd"> - <param name="hbd_min" type="integer" value="" label="Minimum number of HB donors"/> - <param name="hbd_max" type="integer" value="" label="Maximum number of HB donors"/> + <param name="hbd_min" type="integer" value="" label="Minimum number of hydrogen bond donors"/> + <param name="hbd_max" type="integer" value="" label="Maximum number of hydrogen bond donors"/> </when> <when value="hba"> - <param name="hba_min" type="integer" value="" label="Minimum number of HB acceptors"/> - <param name="hba_max" type="integer" value="" label="Maximum number of HB acceptors"/> + <param name="hba_min" type="integer" value="" label="Minimum number of hydrogen bond acceptors"/> + <param name="hba_max" type="integer" value="" label="Maximum number of hydrogen bond acceptors"/> </when> <when value="psa"> - <param name="psa_min" type="integer" value="" label="Minimum threshold for the Total Polar Surface Area"/> - <param name="psa_max" type="integer" value="" label="Maximum threshold for the Total Polar Surface Area"/> + <param name="psa_min" type="integer" value="" label="Minimum threshold for the total polar surface area"/> + <param name="psa_max" type="integer" value="" label="Maximum threshold for the total polar surface area"/> </when> <when value="rotbonds"> <param name="rotbonds_min" type="integer" value="" label="Minimum number of rotatable bonds"/> <param name="rotbonds_max" type="integer" value="" label="Maximum number of rotatable bonds"/> </when> <when value="molwt"> - <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the Molecular Weight"/> - <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the Molecular Weight"/> + <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the molecular weight"/> + <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the molecular weight"/> </when> <when value="logp"> - <param name="logp_min" type="float" value="" label="Minimum threshold value for the log-P"/> - <param name="logp_max" type="float" value="" label="Maximum threshold value for the log-P"/> + <param name="logp_min" type="float" value="" label="Minimum threshold value for log P"/> + <param name="logp_max" type="float" value="" label="Maximum threshold value for log P"/> </when> <when value="mr"> - <param name="mr_min" type="float" value="" label="Minimum threshold value for the Molecular Refractivity"/> - <param name="mr_max" type="float" value="" label="Maximum threshold value for the Molecular Refractivity"/> + <param name="mr_min" type="float" value="" label="Minimum threshold value for the molecular refractivity"/> + <param name="mr_max" type="float" value="" label="Maximum threshold value for the molecular refractivity"/> </when> <when value="atoms"> <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/> @@ -154,9 +154,9 @@ **Hint** -| If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file. +| If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. This should be faster and the file can be reused, although it is larger than a SMILES file. | -| For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value). +| For exact matches use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value). | | Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds).