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annotate silicos_qed.xml @ 1:ab73abead7fa draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:41:23 -0400
parents 5ccd3a432785
children fc45bf8b6e01
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ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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1 <tool id="ctb_silicos_qed" name="Drug-likeness" version="0.2">
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5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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2 <description>quantitative estimation (QED)</description>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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4 <requirements>
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ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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5 <requirement type="package" version="2019.03.1">rdkit</requirement>
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5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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6 </requirements>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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7 <command detect_errors="aggressive">
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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8 <![CDATA[
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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9 python '$__tool_directory__/qed.py'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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10 -i '${infile}'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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11 --method '${method}'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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12 --iformat ${infile.ext}
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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13 -o '${outfile}'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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14 $header
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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15 ]]>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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16 </command>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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17 <inputs>
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ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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18 <param format="smi,sdf" name="infile" type="data" label="Molecule data in SDF or SMILES format" help="Dataset missing? See TIP below"/>
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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19 <param name="method" type="select" label="Method" help="Method for weighting features">
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5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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20 <option value="max">Max weight (QEDw,max)</option>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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21 <option value="mean">Mean weight (QEDw,mo)</option>
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22 <option value="unweighted">Unweighted (QEDw,u)</option>
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5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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23 </param>
1
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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24 <param name="header" type="boolean" label="Include the descriptor names as header" truevalue="--header" falsevalue="" checked="false" />
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5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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25 </inputs>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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26 <outputs>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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27 <data format="tabular" name="outfile" />
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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28 </outputs>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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29 <tests>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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30 <!--
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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31 Test a tabular input with the first line being a comment without a # character to start
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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32 -->
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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33 <test>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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34 <param name="infile" value="qed_test.smi" ftype="smi"/>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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35 <param name="method" value="max"/>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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36 <param name="header" value="True"/>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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37 <output name="outfile" file="qed_test_max.tab" ftype="tabular"/>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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38 </test>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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39 <test>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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40 <param name="infile" value="qed_test.smi" ftype="smi"/>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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41 <param name="method" value="mean"/>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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42 <param name="header" value="True"/>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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43 <output name="outfile" file="qed_test_mean.tab" ftype="tabular"/>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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44 </test>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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45 <test>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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46 <param name="infile" value="qed_test.smi" ftype="smi" />
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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47 <param name="method" value="unweighted"/>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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48 <param name="header" value="True"/>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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49 <output name="outfile" file="qed_test_unweighted.tab" ftype="tabular" />
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50 </test>
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51 </tests>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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52 <help>
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53 <![CDATA[
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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54
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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55 .. class:: infomark
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56
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57 **What this tool does**
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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58
1
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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59 Estimates the drug-likeness of molecules, based on eight commonly used molecular
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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60 properties, and reports a score between 0 (all properties unfavourable) to 1 (all
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61 properties favourable). Two possible methods to weight the features are available
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62 (QED\ :sub:`w,mo`\ , QED\ :sub:`w,max`\), as well as an option to leave features
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63 unweighted (QED\ :sub:`w,u`).
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64
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65 The eight properties used are: molecular weight (MW), octanol–water partition
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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66 coefficient (ALOGP), number of hydrogen bond donors (HBDs), number of hydrogen
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67 bond acceptors (HBAs), molecular polar surface area (PSA), number of rotatable
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68 bonds (ROTBs), number of aromatic rings (AROMs) and number of structural alerts
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69 (ALERTS).
0
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70
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71 -----
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72
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73 .. class:: warningmark
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74
1
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75 **Hint**
0
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76
1
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77 All invalid, blank and comment lines are skipped when performing computations. The
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78 number of skipped lines is displayed in the resulting history item. The method refers
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79 to a set of weights that can be applied to the features. These are derived in the
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80 `original paper`_ describing QED.
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81
0
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82
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83 - QED\ :sub:`w,max` using the set of weights that give maximal information content
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84
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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85 - QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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86
1
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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87 - QED\ :sub:`w,u` with all weights as unity i.e. unweighted.
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88
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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89 .. _original paper: https://www.nature.com/articles/nchem.1243
0
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90
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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91 -----
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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92
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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93 .. class:: infomark
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94
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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95 **Input**
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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96
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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97
1
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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98 | - `SDF format`_
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99 | - `SMILES format`_
0
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100
1
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101 .. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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102 .. _SMILES format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
0
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103
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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104 -----
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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105
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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106 .. class:: infomark
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107
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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108 **Output**
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109
1
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110 A table listing the values of the eight features, the QED score, the name of the
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111 molecule, and the number of Lipinski rules which the molecule obeys.
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112
0
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113 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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114 | MW | ALOGP | HBA | HBD | PSA | ROTB | AROM | ALERTS | QED | NAME | Ro5 |
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115 +========+=======+=====+=====+========+======+======+========+=======+================+=====+
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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116 | 286.34 | 1.092 | 6 | 3 | 101.88 | 4 | 2 | 1 | 0.737 | Abacavir | 0 |
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117 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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118 | 181.21 | 0.481 | 4 | 2 | 83.47 | 5 | 0 | 2 | 0.487 | Acamprosate | 0 |
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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119 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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120 | 336.43 | 2.365 | 5 | 3 | 87.66 | 11 | 1 | 1 | 0.540 | Acebutolol | 0 |
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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121 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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122 | 151.16 | 1.351 | 2 | 2 | 49.33 | 2 | 1 | 1 | 0.633 | Acetaminophen | 0 |
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123 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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124 | 222.25 | 0.225 | 5 | 2 | 115.04 | 3 | 1 | 1 | 0.727 | Acetazolamide | 0 |
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125 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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126 | 324.40 | 3.291 | 4 | 2 | 92.34 | 6 | 1 | 1 | 0.772 | Acetohexamide | 0 |
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127 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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128 | 411.57 | 3.492 | 6 | 1 | 47.02 | 7 | 2 | 1 | 0.688 | Acetophenazine | 0 |
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129 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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130 | 329.37 | 3.327 | 4 | 1 | 39.72 | 4 | 2 | 0 | 0.917 | Paroxetine | 0 |
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131 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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132 | 270.21 | 3.146 | 3 | 1 | 55.13 | 4 | 2 | 0 | 0.915 | Leflunomide | 0 |
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133 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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134
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135
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136
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137 ]]>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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138 </help>
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139 <citations>
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140 <citation type="doi">10.1038/nchem.1243</citation>
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141 </citations>
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142 </tool>