Mercurial > repos > bgruening > ctb_im_o3dalign
comparison o3dalign.xml @ 0:b760f006cb6b draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
author | bgruening |
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date | Tue, 21 Jul 2020 05:24:46 -0400 |
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-1:000000000000 | 0:b760f006cb6b |
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1 <tool id="ctb_im_o3dalign" name="Open 3D Align" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> | |
2 <description>with RDKit</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"><![CDATA[ | |
9 ln -s $molquery ./molquery.sdf && | |
10 o3dAlign | |
11 ./molquery.sdf ##positional arg | |
12 -i '$infile' | |
13 -if sdf | |
14 --qmolidx '$qmolidx' | |
15 $crippen | |
16 -n '$number' | |
17 -t '$threshold' | |
18 -a '$attempts' | |
19 -r '$rmsd' | |
20 -e '$emin' | |
21 --meta | |
22 -of sdf | |
23 -o outp &>> $logfile && | |
24 cat outp_metrics.txt &>> $logfile && | |
25 gzip -d outp.sdf.gz | |
26 ]]></command> | |
27 <inputs> | |
28 <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/> | |
29 <param name="molquery" type="data" format="sdf,mol" label="Mol query file" help="Mol file to align against"/> | |
30 <param name="qmolidx" type="integer" value="1" label="Query molecule index" help="Query molecule index in SD-file if not the first"/> | |
31 <param name="threshold" type="float" min="0" value="1" label="Threshold" help="Score cutoff relative to alignment of query to itself"/> | |
32 <param name="number" type="integer" value="0" label="Number of conformers" help="Number of conformers to generate, if 0 then input structures are assumed to already be)"/> | |
33 <param name="rmsd" type="float" min="0" value="1.0" label="RMSD Threshold" help="Prune RMSD threshold for excluding conformers"/> | |
34 <param name="attempts" type="integer" min="0" value="0" label="Number of attempts" help="If confomers fall below the RMSD threshold, number of attempts at regeneration before giving up."/> | |
35 <param name="emin" type="integer" value="0" label="Energy minimisation iterations" help="Number of EM iterations using the MMFF force field. Default is 0 (i.e. no EM)."/> | |
36 <param name="crippen" type="boolean" label="Crippen" truevalue="--crippen" falsevalue="" help="Use Crippen (logP) contributions"/> | |
37 </inputs> | |
38 | |
39 <expand macro="outputs" /> | |
40 | |
41 <tests> | |
42 <test> | |
43 <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> | |
44 <param name="molquery" value="pyrimethamine.mol" ftype="mol"/> | |
45 <param name="threshold" value="30" /> | |
46 <param name="number" value="2" /> | |
47 <output name="outfile"> | |
48 <assert_contents> | |
49 <has_text text="Fc1ccc(Sc2ccc3c(c4c(Cl)cccc4Cl)c(=O)ncn3n2)c(F)c1"/> | |
50 </assert_contents> | |
51 </output> | |
52 <output name="logfile"> | |
53 <assert_contents> | |
54 <has_text text="Perfect score: 0.0 134.34 CCc1nc(N)nc(N)c1-c1ccc(Cl)cc1 17"/> | |
55 </assert_contents> | |
56 </output> | |
57 </test> | |
58 <test> | |
59 <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> | |
60 <param name="molquery" value="pyrimethamine.mol" ftype="mol"/> | |
61 <param name="threshold" value="30" /> | |
62 <param name="number" value="2" /> | |
63 <param name="crippen" value="--crippen" /> | |
64 <output name="outfile"> | |
65 <assert_contents> | |
66 <has_text text="Fc1ccc(Sc2ccc3c(c4c(Cl)cccc4Cl)c(=O)ncn3n2)c(F)c1"/> | |
67 </assert_contents> | |
68 </output> | |
69 <output name="logfile"> | |
70 <assert_contents> | |
71 <has_text text="Perfect score: 0.0 114.13359999999997 CCc1nc(N)nc(N)c1-c1ccc(Cl)cc1 17"/> | |
72 </assert_contents> | |
73 </output> | |
74 </test> | |
75 </tests> | |
76 <help><![CDATA[ | |
77 | |
78 .. class:: infomark | |
79 | |
80 **What this tool does** | |
81 | |
82 Aligns molecules using RDKit's Open 3D Align. | |
83 | |
84 .. class:: infomark | |
85 | |
86 **Input** | |
87 | |
88 | - Input file in `SDF Format`_ | |
89 | |
90 .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file | |
91 .. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification | |
92 | |
93 ----- | |
94 | |
95 .. class:: infomark | |
96 | |
97 **Output** | |
98 | |
99 SD-file of aligned compounds. | |
100 | |
101 ]]></help> | |
102 <expand macro="citations" /> | |
103 </tool> |