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annotate 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
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children da03b00048b1
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1 <tool id="openbabel_filter" name="Filter" version="@VERSION@.0">
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2 <description> a set of molecules from a file</description>
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive">
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9 <![CDATA[
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10 python '$__tool_directory__/ob_filter.py'
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11 -i '${infile}'
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12 -o '${outfile}'
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13 -iformat "${infile.ext}"
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14 -oformat "${infile.ext}"
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15 --filters '{
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16 #if $filter_methods.filter_methods_opts == "ruleof5":
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17 "hbd" : [0, 5],
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18 "hba" : [0, 10],
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19 "molwt" : [0, 500],
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20 "logp" : [-5, 5],
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21 #elif $filter_methods.filter_methods_opts == "LeadLike":
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22 "rotbonds" : [0, 7],
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23 "molwt" : [0, 350],
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24 "logp" : [-5, 3.5],
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25 #elif $filter_methods.filter_methods_opts == "DrugLike":
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26 "hba" : [0, 10],
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27 "rotbonds" : [0, 8],
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28 "molwt" : [150, 500],
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29 "logp" : [-5, 5],
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30 "psa" : [0, 150],
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31 #elif $filter_methods.filter_methods_opts == "FragmentLike":
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32 "rotbonds" : [0, 5],
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33 "molwt" : [0, 250],
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34 "logp" : [-5, 2.5],
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35 #else:
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36 #for $filter in $filter_methods.filter_set:
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37 #set $filter_selected = $filter.filter_sel.filter_sel_opts
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38 #set $filter_min = $filter_selected + "_min"
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39 #set $filter_max = $filter_selected + "_max"
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40 "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ],
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41 #end for
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42 #end if
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43 }'
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44 ]]>
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45 </command>
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46 <inputs>
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47 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi"
7
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48 label="Select input file (can be previously annotated with the 'Compute physico-chemical properties' tool)"/>
0
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49 <conditional name="filter_methods">
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50 <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set">
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51 <option value="user">User-defined properties</option>
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52 <option value="ruleof5">Lipinski's Rule-of-Five</option>
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53 <option value="LeadLike">Lead-like properties</option>
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54 <option value="DrugLike">Drug-like properties</option>
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55 <option value="FragmentLike">Fragment-like properties</option>
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56 </param>
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57 <when value="ruleof5" />
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58 <when value="LeadLike" />
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59 <when value="DrugLike" />
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60 <when value="FragmentLike" />
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61 <when value="user">
7
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62 <repeat name="filter_set" title="Select custom filters">
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63 <conditional name="filter_sel">
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64 <param name="filter_sel_opts" type="select" label="Select properties to filter">
7
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65 <option value="hbd">Number of hydrogen-bond donor groups</option>
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66 <option value="hba">Number of hydrogen-bond acceptor groups</option>
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67 <option value="psa">Total polar surface area</option>
0
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68 <option value="rotbonds">Number of rotatable bonds</option>
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69 <option value="molwt">Molecular weight</option>
7
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70 <option value="logp">Predicted value of logP</option>
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71 <option value="mr">Predicted value for the molecular refractivity</option>
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72 <option value="atoms">Number of atoms</option>
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73 <!-- Add later, we need to add a new smarts pattern to plugindefines.txt
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74 <option value="hatoms">Number of heavy atoms</option>-->
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75 <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html -->
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76 <!--<option value="rings">Number of rings</option>-->
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77 </param>
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78 <when value="hbd">
7
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79 <param name="hbd_min" type="integer" value="" label="Minimum number of hydrogen bond donors"/>
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80 <param name="hbd_max" type="integer" value="" label="Maximum number of hydrogen bond donors"/>
0
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81 </when>
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82 <when value="hba">
7
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83 <param name="hba_min" type="integer" value="" label="Minimum number of hydrogen bond acceptors"/>
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84 <param name="hba_max" type="integer" value="" label="Maximum number of hydrogen bond acceptors"/>
0
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85 </when>
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86 <when value="psa">
7
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87 <param name="psa_min" type="integer" value="" label="Minimum threshold for the total polar surface area"/>
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88 <param name="psa_max" type="integer" value="" label="Maximum threshold for the total polar surface area"/>
0
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89 </when>
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90 <when value="rotbonds">
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91 <param name="rotbonds_min" type="integer" value="" label="Minimum number of rotatable bonds"/>
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92 <param name="rotbonds_max" type="integer" value="" label="Maximum number of rotatable bonds"/>
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93 </when>
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94 <when value="molwt">
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95 <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the molecular weight"/>
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96 <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the molecular weight"/>
0
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97 </when>
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98 <when value="logp">
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99 <param name="logp_min" type="float" value="" label="Minimum threshold value for log P"/>
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100 <param name="logp_max" type="float" value="" label="Maximum threshold value for log P"/>
0
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101 </when>
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102 <when value="mr">
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103 <param name="mr_min" type="float" value="" label="Minimum threshold value for the molecular refractivity"/>
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104 <param name="mr_max" type="float" value="" label="Maximum threshold value for the molecular refractivity"/>
0
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105 </when>
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106 <when value="atoms">
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107 <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/>
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108 <param name="atoms_max" type="integer" value="" label="Maximum number of atoms"/>
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109 </when>
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110 <!--<when value="rings">
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111 <param name="rings_min" type="integer" value="" label="Minimum number of rings"/>
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112 <param name="rings_max" type="integer" value="" label="Maximum number of rings"/>
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113 </when>-->
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114 </conditional>
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115 </repeat>
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116 </when>
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117 </conditional>
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118 </inputs>
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119 <outputs>
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120 <expand macro="output_like_input"/>
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121 </outputs>
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122 <tests>
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123 <test>
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124 <param name="infile" ftype="smi" value="CID_2244.smi"/>
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125 <param name="filter_methods_opts" value="ruleof5" />
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126 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" />
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127 </test>
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128 <!--
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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129 Limitation of the test framework:
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130 https://trello.com/card/disambiguated-conditional-parameters-not-supported-in-unit-tests/506338ce32ae458f6d15e4b3/820
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131 <test>
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132 <param name="infile" ftype="smi" value="CID_2244.smi"/>
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133 <param name="filter_methods_opts" value="user" />
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134 <param name="filter_sel_opts" value="hba" />
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135 <param name="hbd_min" value="0" />
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136 <param name="hbd_max" value="5" />
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137 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244_2.smi" />
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138 </test>
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139 -->
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140 </tests>
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141 <help>
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142 <![CDATA[
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143
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144
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145 .. class:: infomark
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146
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147 **What this tool does**
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148
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149 Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries.
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150
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151 -----
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152
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153 .. class:: warningmark
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154
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155 **Hint**
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156
7
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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.
0
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158 |
7
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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).
0
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160 |
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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).
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162
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163 -----
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164
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165 .. class:: infomark
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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166
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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167 **Definition of the pre-defined filtering rules**
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168
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169 **# Lipinski's Rule of Five:**
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170 =< 5 Hydrogen-bond donor groups
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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171
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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172 =< 10 Hydrogen-bond acceptor groups
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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173
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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174 =< 500 Molecular weight
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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175
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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176 =< 5 octanol/water partition coefficient (log P)
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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177
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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178 **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748):
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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179 =< 7 rotatable bonds
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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180
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181 =< 350 Molecular weight
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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182
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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183 =< 3.5 octanol/water partition coefficient (log P)
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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184
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185 **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49):
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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186 =< 10 Hydrogen-bond acceptor groups
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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187
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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188 =< 8 rotatable bonds
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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189
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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190 150 =< Molecular weight =< 500
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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191
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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192 =< 150 Polar Surface Area
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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193
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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194 =< 5 octanol/water partition coefficient (log P)
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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195
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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196 **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987):
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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197 =< 5 rotatable bonds
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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198
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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199 =< 250 Molecular weight
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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200
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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201 =< 2.5 octanol/water partition coefficient (log P)
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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202
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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203 -----
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204
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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205 .. class:: infomark
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206
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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207 **Input**
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208
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209 | - `SD-Format`_
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210 | - `SMILES Format`_
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211
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212 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
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213 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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214
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215 -----
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216
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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217 .. class:: infomark
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218
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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219 **Output**
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220
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221 | SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound.
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222 |
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223 | SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound.
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224
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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225
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226
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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227 ]]>
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228 </help>
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229 <expand macro="citations">
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230 <citation type="doi">10.1186/1752-153X-2-5</citation>
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231 </expand>
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232 </tool>