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annotate silicos_qed.xml @ 2:fc45bf8b6e01 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:47:05 -0400
parents ab73abead7fa
children 52a8d34dd08f
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2
fc45bf8b6e01 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="ctb_silicos_qed" name="Drug-likeness" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
fc45bf8b6e01 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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2 <macros>
fc45bf8b6e01 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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3 <token name="@TOOL_VERSION@">2019.03.1</token>
fc45bf8b6e01 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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4 <token name="@GALAXY_VERSION@">0</token>
fc45bf8b6e01 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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5 </macros>
fc45bf8b6e01 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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6 <description>quantitative estimation (QED) 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-->
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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8 <requirements>
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fc45bf8b6e01 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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9 <requirement type="package" version="@TOOL_VERSION@">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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10 </requirements>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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11 <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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12 <![CDATA[
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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13 python '$__tool_directory__/qed.py'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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14 -i '${infile}'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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15 --method '${method}'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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16 --iformat ${infile.ext}
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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17 -o '${outfile}'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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18 $header
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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19 ]]>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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20 </command>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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21 <inputs>
1
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22 <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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23 <param name="method" type="select" label="Method" help="Method for weighting features">
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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24 <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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25 <option value="mean">Mean weight (QEDw,mo)</option>
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26 <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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27 </param>
1
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28 <param name="header" type="boolean" label="Include the descriptor names as header" truevalue="--header" falsevalue="" checked="false" />
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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29 </inputs>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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30 <outputs>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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31 <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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32 </outputs>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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33 <tests>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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34 <!--
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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35 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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36 -->
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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37 <test>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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38 <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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39 <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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40 <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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41 <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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42 </test>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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43 <test>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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44 <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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45 <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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46 <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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47 <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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48 </test>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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49 <test>
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50 <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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51 <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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52 <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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53 <output name="outfile" file="qed_test_unweighted.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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54 </test>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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55 </tests>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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56 <help>
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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57 <![CDATA[
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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58
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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59 .. class:: infomark
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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60
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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61 **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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62
1
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63 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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64 properties, and reports a score between 0 (all properties unfavourable) to 1 (all
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65 properties favourable). Two possible methods to weight the features are available
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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66 (QED\ :sub:`w,mo`\ , QED\ :sub:`w,max`\), as well as an option to leave features
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67 unweighted (QED\ :sub:`w,u`).
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68
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69 The eight properties used are: molecular weight (MW), octanol–water partition
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70 coefficient (ALOGP), number of hydrogen bond donors (HBDs), number of hydrogen
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71 bond acceptors (HBAs), molecular polar surface area (PSA), number of rotatable
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72 bonds (ROTBs), number of aromatic rings (AROMs) and number of structural alerts
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73 (ALERTS).
0
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74
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75 -----
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76
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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77 .. class:: warningmark
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78
1
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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79 **Hint**
0
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80
1
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81 All invalid, blank and comment lines are skipped when performing computations. The
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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82 number of skipped lines is displayed in the resulting history item. The method refers
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83 to a set of weights that can be applied to the features. These are derived in the
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84 `original paper`_ describing QED.
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85
0
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86
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87 - QED\ :sub:`w,max` using the set of weights that give maximal information content
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88
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89 - QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content
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90
1
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91 - QED\ :sub:`w,u` with all weights as unity i.e. unweighted.
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92
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93 .. _original paper: https://www.nature.com/articles/nchem.1243
0
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94
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95 -----
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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96
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97 .. class:: infomark
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98
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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99 **Input**
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100
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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101
1
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102 | - `SDF format`_
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103 | - `SMILES format`_
0
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104
1
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105 .. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
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106 .. _SMILES format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
0
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107
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108 -----
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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109
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110 .. class:: infomark
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111
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112 **Output**
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113
1
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114 A table listing the values of the eight features, the QED score, the name of the
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115 molecule, and the number of Lipinski rules which the molecule obeys.
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116
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 | MW | ALOGP | HBA | HBD | PSA | ROTB | AROM | ALERTS | QED | NAME | Ro5 |
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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 | 286.34 | 1.092 | 6 | 3 | 101.88 | 4 | 2 | 1 | 0.737 | Abacavir | 0 |
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121 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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122 | 181.21 | 0.481 | 4 | 2 | 83.47 | 5 | 0 | 2 | 0.487 | Acamprosate | 0 |
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123 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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124 | 336.43 | 2.365 | 5 | 3 | 87.66 | 11 | 1 | 1 | 0.540 | Acebutolol | 0 |
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125 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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126 | 151.16 | 1.351 | 2 | 2 | 49.33 | 2 | 1 | 1 | 0.633 | Acetaminophen | 0 |
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127 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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128 | 222.25 | 0.225 | 5 | 2 | 115.04 | 3 | 1 | 1 | 0.727 | Acetazolamide | 0 |
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129 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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130 | 324.40 | 3.291 | 4 | 2 | 92.34 | 6 | 1 | 1 | 0.772 | Acetohexamide | 0 |
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131 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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132 | 411.57 | 3.492 | 6 | 1 | 47.02 | 7 | 2 | 1 | 0.688 | Acetophenazine | 0 |
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133 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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134 | 329.37 | 3.327 | 4 | 1 | 39.72 | 4 | 2 | 0 | 0.917 | Paroxetine | 0 |
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135 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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136 | 270.21 | 3.146 | 3 | 1 | 55.13 | 4 | 2 | 0 | 0.915 | Leflunomide | 0 |
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137 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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138
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139
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140
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141 ]]>
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142 </help>
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143 <citations>
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144 <citation type="doi">10.1038/nchem.1243</citation>
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145 </citations>
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146 </tool>