Mercurial > repos > bgruening > ctb_im_xcos

comparison xcos.xml @ 0:73164cea9b60 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
author bgruening
date Tue, 21 Jul 2020 05:22:23 -0400
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children 9b6210854c8c
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-1:000000000000 0:73164cea9b60
1 <tool id="ctb_im_xcos" name="XCos" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>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
11 xcos
12 -if sdf
13 --fragments-format sdf
14 -of sdf
15 --no-gzip
16 -f '$fragments'
17 -i '$poses'
18 -o output
19 ]]>
20 </command>
21 <inputs>
22 <param name="poses" format="sdf" type="data" label="Poses to score" help="In SDF format"/>
23 <param name="fragments" format="sdf" type="data" label="Fragments to compare" help="In SDF format"/>
24 </inputs>
25 <outputs>
26 <data format="sdf" name="output" from_work_dir="output.sdf" />
27 </outputs>
28 <tests>
29 <test>
30 <param name="poses" ftype='sdf' value="poses.sdf" />
31 <param name="fragments" ftype='sdf' value="hits-17.sdf" />
32 <output name="output" ftype='sdf'>
33 <assert_contents>
34 <has_text text="XCos_Score3" />
35 <has_n_lines n="818" />
36 </assert_contents>
37 </output>
38 </test>
39 </tests>
40 <help>
41 <![CDATA[
42
43 .. class:: infomark
44
45 **What this tool does**
46
47 XCos is a reverse shape and feature overlap score for a pose compared to a set of ligands that identifies which ligands
48 best overlap.
49 The molecule is fragmented using the BRICS algorithm and each fragment (bit) is compared to the ligands using the SuCOS
50 methodology. The resulting scores are the combined scores of the bits.
51
52 XCoseScore1 -
53 XCoseScore2 -
54 XCoseScore3 -
55
56 XCos was conceived and implemented by Warren Thompson <warren.thompson@diamond.ac.uk>.
57 The original code can be found here: https://github.com/Waztom/xchem-notebooks/blob/master/XCOS.ipynb
58
59 -----
60
61 .. class:: infomark
62
63 **Input**
64
65 - poses: SD-file of ligand poses to score
66 - fragments: SD-file of fragments to compare the poses
67
68 -----
69
70 .. class:: infomark
71
72 **Output**
73
74 SD-file with the XCos scores added.
75
76
77 ]]>
78 </help>
79 <expand macro="citations" />
80 </tool>