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annotate PaDEL.xml @ 0:30c673b5b061 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
author bgruening
date Tue, 20 Aug 2019 10:58:04 -0400
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children a84bcb007b09
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30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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1 <tool id="padel" name="PaDEL descriptor" version="2.21">
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2 <description>calculator</description>
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3 <requirements>
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4 <requirement type="package" version="2.21">padel</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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7 ln -s '$input' ./molecule.${input.ext} &&
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8
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9 padel
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10 $coordinate2d
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11 $detectaromaticity
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12 $removesalt
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13 $standardizenitro
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14 $convert3d
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15 $retain3d
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16 $coordinate3d
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17 $fingerprint
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18 -retainorder true
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19 -file ./out.csv
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20 -maxruntime 600000
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21 -dir ./molecule.${input.ext}
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22 &&
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23
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24 cat ./out.csv | tr "," "\\t" > '$descriptor'
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25
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26 ]]></command>
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27 <inputs>
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28 <param format="sdf,smi" name="input" type="data" label="SDF or SMILES file" optional= "false"/>
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29
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30 <param name="detectaromaticity" type="boolean" label="Detect aromaticity"
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31 truevalue="-detectaromaticity" falsevalue="" checked="true" help="Remove existing aromaticity information in the molecule before calculation of descriptors."/>
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32
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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33 <param name="removesalt" type="boolean" label="Remove salt"
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34 truevalue="-removesalt" falsevalue="" checked="true" help="Remove salt from molecule(s). Choose No if you have already removed salt from the molecule yourself (recommended)."/>
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35
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36 <param name="standardizenitro" type="boolean" label="Standardize nitro groups"
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37 truevalue="-standardizenitro" falsevalue="" checked="true" help="Standardize nitro groups to N(:O):O."/>
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38
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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39 <param name="convert3d" type="boolean" label="Convert to 3D"
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40 truevalue="-convert3d" falsevalue="" checked="false" help="Convert molecule to 3D representation."/>
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41
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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42 <param name="coordinate2d" type="boolean" label="Calculate 2d descriptors"
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43 truevalue="-2d" falsevalue="" checked="true" help="Calculate 1D and 2D descriptors."/>
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44
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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45 <param name="retain3d" type="boolean" label="Retain 3D coordinates"
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46 truevalue="-retain3d" falsevalue="" checked="false" help="Retain 3D coordinates when standardizing structure."/>
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47
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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48 <param name="coordinate3d" type="boolean" label="Calculate 3d descriptors"
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49 truevalue="-3d" falsevalue="" checked="false" help="Calculate 3D descriptors. To calculate 3D descriptors, the convert molecule to 3D option should be selected."/>
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50
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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51 <param name="fingerprint" type="boolean" label="Calculate fingerprints"
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52 truevalue="-fingerprints" falsevalue="" checked="true" help="Calculate molecular fingerprints."/>
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53
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54 </inputs>
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55 <outputs>
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56 <data format="csv" name="descriptor" label="PaDEL descriptor file for $input.name "/>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="input" value="test.sdf" ftype="sdf"/>
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61 <param name="detectaromaticity" value="-detectaromaticity" />
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62 <param name="removesalt" value="-removesalt" />
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63 <param name="standardizenitro" value="-standardizenitro" />
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64 <param name="convert3d" value="" />
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65 <param name="retain3d" value="" />
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66 <param name="maxruntime" value="600000" />
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67 <param name="coordinate2d" value="-2d" />
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68 <param name="coordinate3d" value="" />
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69 <param name="fingerprint" value="" />
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70 <param name="retainorder" value="-retainorder" />
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71 <output name="descriptor">
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72 <assert_contents>
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73 <has_n_columns n="1445" />
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74 <has_text text="3.735268" />
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75 <has_text text="13.148254" />
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76 <has_text text="0.38897" />
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77 <has_text text="-0.00131" />
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78 </assert_contents>
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79 </output>
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80 </test>
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81 <test>
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82 <param name="input" value="test.sdf" ftype="sdf"/>
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83 <param name="detectaromaticity" value="-detectaromaticity" />
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84 <param name="removesalt" value="-removesalt" />
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85 <param name="standardizenitro" value="-standardizenitro" />
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86 <param name="convert3d" value="" />
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87 <param name="retain3d" value="" />
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88 <param name="maxruntime" value="600000" />
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89 <param name="coordinate2d" value="-2d" />
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90 <param name="coordinate3d" value="" />
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91 <param name="fingerprint" value="-fingerprints" />
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92 <param name="retainorder" value="-retainorder" />
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93 <output name="descriptor">
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94 <assert_contents>
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95 <has_n_columns n="2326" />
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96 <has_text text="1.17828" />
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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97 <has_text text="2.77182" />
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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98 <has_text text="-1.06144" />
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99 <has_text text="-5.91478" />
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100 </assert_contents>
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101 </output>
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102 </test>
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103 <test>
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104 <param name="input" value="test.sdf" ftype="sdf"/>
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105 <param name="detectaromaticity" value="" />
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106 <param name="removesalt" value="-removesalt" />
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107 <param name="standardizenitro" value="-standardizenitro" />
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108 <param name="convert3d" value="" />
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109 <param name="retain3d" value="" />
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110 <param name="maxruntime" value="600000" />
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111 <param name="coordinate2d" value="-2d" />
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112 <param name="coordinate3d" value="" />
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113 <param name="fingerprint" value="-fingerprints" />
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114 <param name="retainorder" value="-retainorder" />
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115 <output name="descriptor">
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116 <assert_contents>
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117 <has_n_columns n="2326" />
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118 <has_text text="0.93896" />
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119 <has_text text="2.85714" />
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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120 <has_text text="-33.59391" />
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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121 <has_text text="11.62754" />
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122 </assert_contents>
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123 </output>
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124 </test>
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125 </tests>
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126 <help><![CDATA[
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127
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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128 The PaDEL descriptor tool calculates different kinds of molecular descriptors and fingerprints, using the Chemistry Development Kit (CDK). Descriptors include atom type, electrotopological state descriptors, Crippen's logP and MR, extended topochemical atom (ETA) descriptors, McGowan volume, molecular linear free energy relation descriptors, ring counts, count of chemical substructures identified by Laggner, binary fingerprints and count of chemical substructures. For more details, please consult the cited publication.
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129
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130 -----
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131
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132 .. class:: infomark
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133
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134 **Input**
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135
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136 - SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
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137 - SMILES Format: http://www.molecular-networks.com/products/corina
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138
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139 -----
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140
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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141 .. class:: infomark
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142
30c673b5b061 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
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143 **Output**
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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 ]]></help>
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147 <citations>
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148 <citation type="bibtex">
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149 @article{rdkit,
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150 author = {Chun Wei Yap},
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151 title = {PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints},
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152 url ={https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21707}
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153 }</citation>
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154 </citations>
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155 </tool>