Mercurial > repos > bgruening > ctb_rdkit_descriptors

annotate rdkit_descriptors.xml @ 7:cf725c82c865 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:43:19 -0400
parents 6674260c1459
children a1c53f0533b0
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rev   line source
7
cf725c82c865 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="ctb_rdkit_descriptors" name="Descriptors" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
cf725c82c865 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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2 <macros>
cf725c82c865 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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3 <token name="@TOOL_VERSION@">2020.03.4</token>
cf725c82c865 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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4 <token name="@GALAXY_VERSION@">0</token>
cf725c82c865 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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5 </macros>
0
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6 <description>calculated with RDKit</description>
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7 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
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8 <requirements>
7
cf725c82c865 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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9 <requirement type="package" version="@TOOL_VERSION@">rdkit</requirement>
0
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10 </requirements>
1
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11 <command detect_errors="exit_code">
0
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12 <![CDATA[
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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13 python '$__tool_directory__/rdkit_descriptors.py'
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14 -i '${infile}'
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15 --iformat '${infile.ext}'
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16 -o '${outfile}'
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17 $header
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="infile" format="smi,sdf,mol2" type="data" label="Molecule data"
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22 help="In SDF or SMILES format"/>
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23 <param name="header" type="boolean" label="Include the descriptor name as header"
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24 truevalue="--header" falsevalue="" checked="false" />
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25 </inputs>
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26 <outputs>
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27 <data format="tabular" name="outfile" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="infile" ftype='sdf' value="CID_3037.sdf" />
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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32 <param name="header" value="True" />
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33 <output name="outfile" ftype='tabular' file="rdkit_descriptors_result1.tab" />
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34 </test>
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35 </tests>
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36 <help>
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37 <![CDATA[
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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38
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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39 .. class:: infomark
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40
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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41 **What this tool does**
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42
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43 | RDKit is an open source toolkit for cheminformatics and machine learning.
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44 | This tool calculates various molecular descriptors for the input data. The table below shows a brief overview of the descriptors.
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45 |
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46
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47 +-----------------------------------+------------+
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48 | Descriptor/Descriptor Family | Language |
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49 +===================================+============+
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50 | Gasteiger/Marsili Partial Charges | C++ |
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51 +-----------------------------------+------------+
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52 | BalabanJ | Python |
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53 +-----------------------------------+------------+
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54 | BertzCT | Python |
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55 +-----------------------------------+------------+
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56 | Ipc | Python |
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57 +-----------------------------------+------------+
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58 | HallKierAlpha | Python |
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59 +-----------------------------------+------------+
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60 | Kappa1 - Kappa3 | Python |
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61 +-----------------------------------+------------+
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62 | Chi0, Chi1 | Python |
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63 +-----------------------------------+------------+
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64 | Chi0n - Chi4n | Python |
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65 +-----------------------------------+------------+
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66 | Chi0v - Chi4v | Python |
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67 +-----------------------------------+------------+
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68 | MolLogP | C++ |
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69 +-----------------------------------+------------+
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70 | MolMR | C++ |
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71 +-----------------------------------+------------+
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72 | MolWt | C++ |
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73 +-----------------------------------+------------+
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74 | HeavyAtomCount | Python |
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75 +-----------------------------------+------------+
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76 | HeavyAtomMolWt | Python |
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77 +-----------------------------------+------------+
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78 | NHOHCount | C++ |
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79 +-----------------------------------+------------+
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80 | NOCount | C++ |
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81 +-----------------------------------+------------+
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82 | NumHAcceptors | C++ |
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83 +-----------------------------------+------------+
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84 | NumHDonors | C++ |
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85 +-----------------------------------+------------+
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86 | NumHeteroatoms | C++ |
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87 +-----------------------------------+------------+
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88 | NumRotatableBonds | C++ |
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89 +-----------------------------------+------------+
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90 | NumValenceElectrons | Python |
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91 +-----------------------------------+------------+
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92 | RingCount | C++ |
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93 +-----------------------------------+------------+
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94 | TPSA | C++ |
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95 +-----------------------------------+------------+
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96 | LabuteASA | C++ |
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97 +-----------------------------------+------------+
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98 | PEOE_VSA1 - PEOE_VSA14 | Python/C++ |
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99 +-----------------------------------+------------+
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100 | SMR_VSA1 - SMR_VSA10 | Python/C++ |
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101 +-----------------------------------+------------+
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102 | SlogP_VSA1 - SlogP_VSA12 | Python/C++ |
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103 +-----------------------------------+------------+
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104 | EState_VSA1 - EState_VSA11 | Python |
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105 +-----------------------------------+------------+
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106 | VSA_EState1 - VSA_EState10 | Python |
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107 +-----------------------------------+------------+
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108 | Topliss fragments | Python |
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109 +-----------------------------------+------------+
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110
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111 |
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112 | A full list of the descriptors can be obtained here_.
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113
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114 .. _here: https://rdkit.readthedocs.org/en/latest/GettingStartedInPython.html#list-of-available-descriptors
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115
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116 -----
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117
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118 .. class:: warningmark
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119
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120 **Hint**
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121
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122 Use the **cut columns from a table** tool to select just the desired descriptors.
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123
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124 -----
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125
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126 .. class:: infomark
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127
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128 **Input**
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129
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130 | - `SDF Format`_
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131 | - `SMILES Format`_
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132 | - `Corina MOL2`_
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133
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134 .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
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135 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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136 .. _Corina MOL2: http://www.molecular-networks.com/products/corina
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137
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138 -----
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139
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140 .. class:: infomark
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141
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142 **Output**
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143
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144 Tabular file, where each descriptor (value) is shown in a separate column.
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145
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146
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147 ]]>
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148 </help>
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149 <citations>
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150 <citation type="bibtex">
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151 @article{rdkit,
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152 author = {Greg Landrum and others},
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153 title = {RDKit: Open-source cheminformatics},
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154 url ={http://www.rdkit.org}
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155 }</citation>
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156 </citations>
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157 </tool>