Mercurial > repos > bgruening > sucos_docking_scoring

comparison sucos.xml @ 0:f8f53668d5a2 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
author bgruening
date Wed, 02 Oct 2019 12:58:43 -0400
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-1:000000000000 0:f8f53668d5a2
1 <tool id="sucos_docking_scoring" name="Score docked poses using SuCOS" version="0.1">
2 <description>- compare shape and feature overlap of docked ligand poses to a reference molecule</description>
3 <macros>
4 <import>sucos_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="aggressive"><![CDATA[
8 python '$__tool_directory__/sucos.py'
9 -i '$input'
10 -r '$refmol'
11 -o '$output'
12 --refmol-format mol
13 $tanimoto
14 ]]></command>
15 <inputs>
16 <param type="data" name="input" format="sdf" label="Ligands to be scored" help="Input in SDF format." />
17 <param type="data" name="refmol" format="sdf,mol" label="Reference molecule to overlay" help="Input in SDF or MOL format." />
18 <param type="boolean" name="tanimoto" truevalue="--tanimoto" falsevalue="" label="Include Tanimoto calculations" help="Whether to handle the distance as Tanimoto." />
19 </inputs>
20 <outputs>
21 <data format="sdf" name="output" label="The scored ligands"/>
22 </outputs>
23 <tests>
24 <test>
25 <param name="input" ftype="sdf" value="sucos_inputs.sdf"/>
26 <param name="refmol" ftype="mol" value="sucos_refmol.mol"/>
27 <output name="output" ftype="sdf">
28 <assert_contents>
29 <has_text text="SuCOS_Score" />
30 </assert_contents>
31 </output>
32 </test>
33 </tests>
34 <help><![CDATA[
35 .. class:: infomark
36
37 **What it does**
38
39 This tool determines the shape and feature overlap of docked ligand poses compared to a reference molecule, usually a known ligand.
40 The RDKit FeatureMap functionality is used to do the scoring.
41
42 The original SuCOS code is on GitHub_ under a MIT license. The SuCOS work is described here_.
43
44 .. _GitHub: https://github.com/susanhleung/SuCOS
45 .. _here: https://chemrxiv.org/articles/SuCOS_is_Better_than_RMSD_for_Evaluating_Fragment_Elaboration_and_Docking_Poses/8100203
46
47 .. class:: infomark
48
49 **Input**
50
51 Molecules such as an SD file dataset from the history.
52
53 .. class:: infomark
54
55 **Output**
56
57 The same SD file with a "SuCOS_Score" property added. A score of 1.0 infers a perfect overlap, a score of 0.0 no overlap.
58 A rule of thumb is that poses with a score greater than 0.5 can be be considered "useful".
59
60 ]]></help>
61 <expand macro="citations"/>
62 </tool>
63