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comparison sucos_max.xml @ 0:bb5365381c8f 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 12:57:54 -0400
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1 <tool id="sucos_max_score" name="Max SuCOS score" version="0.1">
2 <description>- determine maximum SuCOS score of ligands against clustered fragment hits</description>
3 <macros>
4 <import>sucos_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="aggressive"><![CDATA[
8 python '$__tool_directory__/sucos_max.py'
9 -i '$input'
10 -o '$output'
11 -m $mode
12 #for $cluster in $clusters
13 '$cluster'
14 #end for
15 ]]></command>
16 <inputs>
17 <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." />
18 <param name="clusters" type="data" format="sdf" multiple="true" label="Set of clusters to score against" help="Clusters in SDF format." />
19 <param name="mode" type="select" value="max" label="Mode">
20 <option value="max">Max score</option>
21 <option value="cum">Cumulative score</option>
22 </param>
23 </inputs>
24 <outputs>
25 <data format="sdf" name="output" label="The scored ligands"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
30 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
31 <param name="mode" value="max"/>
32 <output name="output" ftype="sdf">
33 <assert_contents>
34 <has_text text="Max_SuCOS_Score" />
35 </assert_contents>
36 </output>
37 </test>
38 <test>
39 <param name="input" ftype="sdf" value="sucos_cluster.sdf"/>
40 <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/>
41 <param name="mode" value="cum"/>
42 <output name="output" ftype="sdf">
43 <assert_contents>
44 <has_text text="Cum_SuCOS_Score" />
45 </assert_contents>
46 </output>
47 </test>
48 </tests>
49 <help><![CDATA[
50
51 .. class:: infomark
52
53 **What it does**
54
55 This tool determines the maximum SuCOS score of ligands, presumed to be potential follow on compounds, compared to a
56 set of clustered reference compounds, presumed to be fragment screening hits. Each ligand to be scored is compared to
57 all of the reference compounds with the highest score being recorded, along with the cluster it came from and the index
58 of the molecule within that cluster.
59
60 The original SuCOS code is on GitHub_ under a MIT license. The SuCOS work is described here_.
61
62 .. _GitHub: https://github.com/susanhleung/SuCOS
63 .. _here: https://chemrxiv.org/articles/SuCOS_is_Better_than_RMSD_for_Evaluating_Fragment_Elaboration_and_Docking_Poses/8100203
64
65 .. class:: infomark
66
67 **Input**
68
69 The clustered reference compounds are likely to have been generated using the "Cluster ligands using SuCOS" tool and
70 will comprise a SDF format file for each cluster. The ligands to be scored are supplied in a SDF file.
71
72 .. class:: infomark
73
74 **Output**
75
76 The same SD file as the input ligands with a "Max_SuCOS_Score" property added containing the best (maximum) SuCOS score
77 along with the "Max_SuCOS_FeatureMap_Score" and "Max_SuCOS_Tanimoto_Score" of that comparison.
78
79 In addition, the "Max_SuCOS_Cluster" field shows the name of the cluster file that contained the molecule with this best
80 score and the "Max_SuCOS_Index" shows the index (first record is index 1) of that molecule in the file.
81
82 ]]></help>
83 <expand macro="citations"/>
84 </tool>
85