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comparison featurestein.xml @ 0:a84113368c6d draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
author bgruening
date Mon, 27 Jul 2020 15:24:43 +0000
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-1:000000000000 0:a84113368c6d
1 <tool id="featurestein" name="'FeatureStein' fragment overlay scoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>feature overlay scoring</description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code">
9 <![CDATA[
10 featurestein_generate -i '$fragments' -if sdf &&
11 featurestein_score -i '$ligands' -if sdf -f featurestein.p -o output -of sdf --no-gzip
12 ]]>
13 </command>
14 <inputs>
15 <param name="fragments" format="sdf" type="data" label="Fragments to generate feature maps" help="In SDF format"/>
16 <param name="ligands" format="sdf" type="data" label="Ligands to score" help="In SDF format"/>
17 </inputs>
18 <outputs>
19 <data name="output" format="sdf" from_work_dir="output.sdf" label="The scored ligands"/>
20 </outputs>
21 <tests>
22 <test>
23 <param name="fragments" ftype='sdf' value="hits-17.sdf" />
24 <param name="ligands" ftype='sdf' value="poses.sdf" />
25 <output name="output" ftype="sdf">
26 <assert_contents>
27 <has_n_lines n="692" />
28 <has_text text="FeatureStein_Qual" />
29 <has_text text="FeatureStein_Quant" />
30 </assert_contents>
31 </output>
32 </test>
33 </tests>
34 <help>
35 <![CDATA[
36
37 .. class:: infomark
38
39 **What this tool does**
40
41 FeatureStein involves use of merged RDKit feature maps to score ligand poses in terms of how well the features overlap
42 with features from a set of ligands, typically fragment screening hits. The features are molecular features like
43 hydrogen bond donors and acceptors or hydrophobic groups.
44 See this Jupyter notebook for more information: https://github.com/tdudgeon/jupyter_mpro/blob/master/featurestein/FeatureStein.ipynb
45 and this blog for more general info on RDKit feature maps:
46 http://rdkit.blogspot.com/2017/11/using-feature-maps.html
47
48 This module generates the merged feature maps from a set of molecules (typically fragment screening hits) and then.
49 scores a set of ligands using those merged feature maps.
50
51 The fields that are created are:
52
53 - FeatureStein_Quant: the sum of the scores for each feature in the ligand
54 - FeatureStein_Qual: the FeatureStein_Quant score divided by the number of features (number between 0 and 1)
55
56 -----
57
58 .. class:: infomark
59
60 **Input**
61
62 - fragments: SD-file of fragments to generate feature maps and merge
63 - ligands: SD-file of ligands to score
64
65 -----
66
67 .. class:: infomark
68
69 **Output**
70
71 SD-file of the ligands with the FeatureStein scores added.
72
73 ]]>
74 </help>
75 <expand macro="citations" />
76 </tool>