Mercurial > repos > bgruening > ctb_rdkit_descriptors

annotate rdkit_descriptors.xml @ 2:6674260c1459 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 3372cca3d07562b643b8152d489dcbd2325acf4a
author bgruening
date Thu, 23 May 2019 18:57:30 -0400
parents 13c6f797f1c3
children cf725c82c865
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6674260c1459 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 3372cca3d07562b643b8152d489dcbd2325acf4a
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1 <tool id="ctb_rdkit_descriptors" name="Descriptors" version="0.6">
0
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2 <description>calculated with RDKit</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 <requirements>
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5 <requirement type="package" version="2019.03.1">rdkit</requirement>
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749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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7 </requirements>
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8 <command detect_errors="exit_code">
0
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9 <![CDATA[
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10 python '$__tool_directory__/rdkit_descriptors.py'
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11 -i '${infile}'
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12 --iformat '${infile.ext}'
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13 -o '${outfile}'
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14 $header
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="infile" format="smi,sdf,mol2" type="data" label="Molecule data"
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19 help="In SDF or SMILES format"/>
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20 <param name="header" type="boolean" label="Include the descriptor name as header"
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21 truevalue="--header" falsevalue="" checked="false" />
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22 </inputs>
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23 <outputs>
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24 <data format="tabular" name="outfile" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="infile" ftype='sdf' value="CID_3037.sdf" />
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29 <param name="header" value="True" />
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30 <output name="outfile" ftype='tabular' file="rdkit_descriptors_result1.tab" />
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31 </test>
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32 </tests>
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33 <help>
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34 <![CDATA[
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35
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36 .. class:: infomark
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38 **What this tool does**
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39
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40 | RDKit is an open source toolkit for cheminformatics and machine learning.
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41 | This tool calculates various molecular descriptors for the input data. The table below shows a brief overview of the descriptors.
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42 |
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43
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44 +-----------------------------------+------------+
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45 | Descriptor/Descriptor Family | Language |
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46 +===================================+============+
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47 | Gasteiger/Marsili Partial Charges | C++ |
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48 +-----------------------------------+------------+
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49 | BalabanJ | Python |
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50 +-----------------------------------+------------+
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51 | BertzCT | Python |
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52 +-----------------------------------+------------+
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53 | Ipc | Python |
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54 +-----------------------------------+------------+
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55 | HallKierAlpha | Python |
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56 +-----------------------------------+------------+
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57 | Kappa1 - Kappa3 | Python |
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58 +-----------------------------------+------------+
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59 | Chi0, Chi1 | Python |
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60 +-----------------------------------+------------+
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61 | Chi0n - Chi4n | Python |
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62 +-----------------------------------+------------+
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63 | Chi0v - Chi4v | Python |
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64 +-----------------------------------+------------+
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65 | MolLogP | C++ |
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66 +-----------------------------------+------------+
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67 | MolMR | C++ |
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68 +-----------------------------------+------------+
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69 | MolWt | C++ |
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70 +-----------------------------------+------------+
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71 | HeavyAtomCount | Python |
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72 +-----------------------------------+------------+
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73 | HeavyAtomMolWt | Python |
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74 +-----------------------------------+------------+
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75 | NHOHCount | C++ |
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76 +-----------------------------------+------------+
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77 | NOCount | C++ |
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78 +-----------------------------------+------------+
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79 | NumHAcceptors | C++ |
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80 +-----------------------------------+------------+
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81 | NumHDonors | C++ |
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82 +-----------------------------------+------------+
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83 | NumHeteroatoms | C++ |
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84 +-----------------------------------+------------+
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85 | NumRotatableBonds | C++ |
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86 +-----------------------------------+------------+
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87 | NumValenceElectrons | Python |
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88 +-----------------------------------+------------+
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89 | RingCount | C++ |
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90 +-----------------------------------+------------+
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91 | TPSA | C++ |
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92 +-----------------------------------+------------+
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93 | LabuteASA | C++ |
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94 +-----------------------------------+------------+
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95 | PEOE_VSA1 - PEOE_VSA14 | Python/C++ |
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96 +-----------------------------------+------------+
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97 | SMR_VSA1 - SMR_VSA10 | Python/C++ |
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98 +-----------------------------------+------------+
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99 | SlogP_VSA1 - SlogP_VSA12 | Python/C++ |
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100 +-----------------------------------+------------+
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101 | EState_VSA1 - EState_VSA11 | Python |
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102 +-----------------------------------+------------+
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103 | VSA_EState1 - VSA_EState10 | Python |
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104 +-----------------------------------+------------+
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105 | Topliss fragments | Python |
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106 +-----------------------------------+------------+
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107
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108 |
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109 | A full list of the descriptors can be obtained here_.
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110
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111 .. _here: https://rdkit.readthedocs.org/en/latest/GettingStartedInPython.html#list-of-available-descriptors
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112
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113 -----
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114
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115 .. class:: warningmark
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116
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117 **Hint**
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118
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119 Use the **cut columns from a table** tool to select just the desired descriptors.
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120
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121 -----
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122
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123 .. class:: infomark
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124
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125 **Input**
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126
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127 | - `SDF Format`_
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128 | - `SMILES Format`_
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129 | - `Corina MOL2`_
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130
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131 .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
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132 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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133 .. _Corina MOL2: http://www.molecular-networks.com/products/corina
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134
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135 -----
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136
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137 .. class:: infomark
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138
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139 **Output**
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140
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141 Tabular file, where each descriptor (value) is shown in a separate column.
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142
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143
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144 ]]>
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145 </help>
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146 <citations>
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147 <citation type="bibtex">
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148 @article{rdkit,
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149 author = {Greg Landrum and others},
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150 title = {RDKit: Open-source cheminformatics},
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151 url ={http://www.rdkit.org}
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152 }</citation>
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153 </citations>
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154 </tool>