Mercurial > repos > bgruening > ctb_im_xcos

annotate xcos.xml @ 1:9b6210854c8c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
author bgruening
date Mon, 27 Jul 2020 11:30:49 -0400
parents 73164cea9b60
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
1 <tool id="ctb_im_xcos" name="XCos" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
2 <description>scoring</description>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
3 <macros>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
4 <import>macros.xml</import>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
5 <token name="@GALAXY_VERSION@">0</token>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
6 </macros>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
7 <expand macro="requirements" />
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
8 <command detect_errors="exit_code">
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
9 <![CDATA[
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
10
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
11 xcos
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
12 -if sdf
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
13 --fragments-format sdf
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
14 -of sdf
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
15 --no-gzip
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
16 -f '$fragments'
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
17 -i '$poses'
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
18 -o output
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
19 ]]>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
20 </command>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
21 <inputs>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
22 <param name="poses" format="sdf" type="data" label="Poses to score" help="In SDF format"/>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
23 <param name="fragments" format="sdf" type="data" label="Fragments to compare" help="In SDF format"/>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
24 </inputs>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
25 <outputs>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
26 <data format="sdf" name="output" from_work_dir="output.sdf" />
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
27 </outputs>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
28 <tests>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
29 <test>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
30 <param name="poses" ftype='sdf' value="poses.sdf" />
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
31 <param name="fragments" ftype='sdf' value="hits-17.sdf" />
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
32 <output name="output" ftype='sdf'>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
33 <assert_contents>
1
9b6210854c8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
bgruening
parents: 0
diff changeset
34 <has_text text="XCos_RefMols" />
9b6210854c8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
bgruening
parents: 0
diff changeset
35 <has_text text="XCos_NumHits" />
9b6210854c8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
bgruening
parents: 0
diff changeset
36 <has_text text="XCos_Score1" />
9b6210854c8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
bgruening
parents: 0
diff changeset
37 <has_n_lines n="734" />
0
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
38 </assert_contents>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
39 </output>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
40 </test>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
41 </tests>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
42 <help>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
43 <![CDATA[
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
44
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
45 .. class:: infomark
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
46
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
47 **What this tool does**
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
48
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
49 XCos is a reverse shape and feature overlap score for a pose compared to a set of ligands that identifies which ligands
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
50 best overlap.
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
51 The molecule is fragmented using the BRICS algorithm and each fragment (bit) is compared to the ligands using the SuCOS
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
52 methodology. The resulting scores are the combined scores of the bits.
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
53
1
9b6210854c8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
bgruening
parents: 0
diff changeset
54 XCos_RefMols - The fragments that the ligand overlays
9b6210854c8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
bgruening
parents: 0
diff changeset
55 XCos_NumHits - the number of fragments the ligand overlays
9b6210854c8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
bgruening
parents: 0
diff changeset
56 XCos_Score1 - The sum of each bit's feature and shape overlay score scaled by the number of heavy bit atoms.
0
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
57
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
58 XCos was conceived and implemented by Warren Thompson <warren.thompson@diamond.ac.uk>.
1
9b6210854c8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
bgruening
parents: 0
diff changeset
59 The original code can be found here: https://github.com/Waztom/xchem-XCOS
0
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
60
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
61 -----
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
62
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
63 .. class:: infomark
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
64
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
65 **Input**
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
66
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
67 - poses: SD-file of ligand poses to score
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
68 - fragments: SD-file of fragments to compare the poses
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
69
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
70 -----
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
71
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
72 .. class:: infomark
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
73
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
74 **Output**
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
75
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
76 SD-file with the XCos scores added.
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
77
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
78
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
79 ]]>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
80 </help>
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
81 <expand macro="citations" />
73164cea9b60 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
bgruening
parents:
diff changeset
82 </tool>