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comparison ob_filter.xml @ 7:0e382252d23d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:35:05 -0400
parents 0d6e836460be
children da03b00048b1
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6:69e02cf88856 7:0e382252d23d
43 }' 43 }'
44 ]]> 44 ]]>
45 </command> 45 </command>
46 <inputs> 46 <inputs>
47 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" 47 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi"
48 label="Select input file previously annotated with the 'Compute physico-chemical properties' tool"/> 48 label="Select input file (can be previously annotated with the 'Compute physico-chemical properties' tool)"/>
49 <conditional name="filter_methods"> 49 <conditional name="filter_methods">
50 <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set"> 50 <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set">
51 <option value="user">User-defined properties</option> 51 <option value="user">User-defined properties</option>
52 <option value="ruleof5">Lipinski's Rule-of-Five</option> 52 <option value="ruleof5">Lipinski's Rule-of-Five</option>
53 <option value="LeadLike">Lead-like properties</option> 53 <option value="LeadLike">Lead-like properties</option>
57 <when value="ruleof5" /> 57 <when value="ruleof5" />
58 <when value="LeadLike" /> 58 <when value="LeadLike" />
59 <when value="DrugLike" /> 59 <when value="DrugLike" />
60 <when value="FragmentLike" /> 60 <when value="FragmentLike" />
61 <when value="user"> 61 <when value="user">
62 <repeat name="filter_set" title="Filters selection"> 62 <repeat name="filter_set" title="Select custom filters">
63 <conditional name="filter_sel"> 63 <conditional name="filter_sel">
64 <param name="filter_sel_opts" type="select" label="Select properties to filter"> 64 <param name="filter_sel_opts" type="select" label="Select properties to filter">
65 <option value="hbd">Number of Hydrogen-bond donor groups</option> 65 <option value="hbd">Number of hydrogen-bond donor groups</option>
66 <option value="hba">Number of Hydrogen-bond acceptor groups</option> 66 <option value="hba">Number of hydrogen-bond acceptor groups</option>
67 <option value="psa">Total polar Surface Area</option> 67 <option value="psa">Total polar surface area</option>
68 <option value="rotbonds">Number of rotatable bonds</option> 68 <option value="rotbonds">Number of rotatable bonds</option>
69 <option value="molwt">Molecular weight</option> 69 <option value="molwt">Molecular weight</option>
70 <option value="logp">Predicted value of LogP</option> 70 <option value="logp">Predicted value of logP</option>
71 <option value="mr">Predicted value for the Molecular Refractivity</option> 71 <option value="mr">Predicted value for the molecular refractivity</option>
72 <option value="atoms">Number of atoms</option> 72 <option value="atoms">Number of atoms</option>
73 <!-- Add later, we need to add a new smarts pattern to plugindefines.txt 73 <!-- Add later, we need to add a new smarts pattern to plugindefines.txt
74 <option value="hatoms">Number of heavy atoms</option>--> 74 <option value="hatoms">Number of heavy atoms</option>-->
75 <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html --> 75 <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html -->
76 <!--<option value="rings">Number of rings</option>--> 76 <!--<option value="rings">Number of rings</option>-->
77 </param> 77 </param>
78 <when value="hbd"> 78 <when value="hbd">
79 <param name="hbd_min" type="integer" value="" label="Minimum number of HB donors"/> 79 <param name="hbd_min" type="integer" value="" label="Minimum number of hydrogen bond donors"/>
80 <param name="hbd_max" type="integer" value="" label="Maximum number of HB donors"/> 80 <param name="hbd_max" type="integer" value="" label="Maximum number of hydrogen bond donors"/>
81 </when> 81 </when>
82 <when value="hba"> 82 <when value="hba">
83 <param name="hba_min" type="integer" value="" label="Minimum number of HB acceptors"/> 83 <param name="hba_min" type="integer" value="" label="Minimum number of hydrogen bond acceptors"/>
84 <param name="hba_max" type="integer" value="" label="Maximum number of HB acceptors"/> 84 <param name="hba_max" type="integer" value="" label="Maximum number of hydrogen bond acceptors"/>
85 </when> 85 </when>
86 <when value="psa"> 86 <when value="psa">
87 <param name="psa_min" type="integer" value="" label="Minimum threshold for the Total Polar Surface Area"/> 87 <param name="psa_min" type="integer" value="" label="Minimum threshold for the total polar surface area"/>
88 <param name="psa_max" type="integer" value="" label="Maximum threshold for the Total Polar Surface Area"/> 88 <param name="psa_max" type="integer" value="" label="Maximum threshold for the total polar surface area"/>
89 </when> 89 </when>
90 <when value="rotbonds"> 90 <when value="rotbonds">
91 <param name="rotbonds_min" type="integer" value="" label="Minimum number of rotatable bonds"/> 91 <param name="rotbonds_min" type="integer" value="" label="Minimum number of rotatable bonds"/>
92 <param name="rotbonds_max" type="integer" value="" label="Maximum number of rotatable bonds"/> 92 <param name="rotbonds_max" type="integer" value="" label="Maximum number of rotatable bonds"/>
93 </when> 93 </when>
94 <when value="molwt"> 94 <when value="molwt">
95 <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the Molecular Weight"/> 95 <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the molecular weight"/>
96 <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the Molecular Weight"/> 96 <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the molecular weight"/>
97 </when> 97 </when>
98 <when value="logp"> 98 <when value="logp">
99 <param name="logp_min" type="float" value="" label="Minimum threshold value for the log-P"/> 99 <param name="logp_min" type="float" value="" label="Minimum threshold value for log P"/>
100 <param name="logp_max" type="float" value="" label="Maximum threshold value for the log-P"/> 100 <param name="logp_max" type="float" value="" label="Maximum threshold value for log P"/>
101 </when> 101 </when>
102 <when value="mr"> 102 <when value="mr">
103 <param name="mr_min" type="float" value="" label="Minimum threshold value for the Molecular Refractivity"/> 103 <param name="mr_min" type="float" value="" label="Minimum threshold value for the molecular refractivity"/>
104 <param name="mr_max" type="float" value="" label="Maximum threshold value for the Molecular Refractivity"/> 104 <param name="mr_max" type="float" value="" label="Maximum threshold value for the molecular refractivity"/>
105 </when> 105 </when>
106 <when value="atoms"> 106 <when value="atoms">
107 <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/> 107 <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/>
108 <param name="atoms_max" type="integer" value="" label="Maximum number of atoms"/> 108 <param name="atoms_max" type="integer" value="" label="Maximum number of atoms"/>
109 </when> 109 </when>
152 152
153 .. class:: warningmark 153 .. class:: warningmark
154 154
155 **Hint** 155 **Hint**
156 156
157 | 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. 157 | 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.
158 | 158 |
159 | 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). 159 | 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).
160 | 160 |
161 | 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). 161 | 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).
162 162
163 ----- 163 -----
164 164