Mercurial > repos > bgruening > ctb_im_constrained_conf_gen
comparison constrained_conf_gen.xml @ 0:9c5121dd2fd4 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
author | bgruening |
---|---|
date | Tue, 21 Jul 2020 05:25:31 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:9c5121dd2fd4 |
---|---|
1 <tool id="ctb_im_constrained_conf_gen" name="Constrained conformer generation" 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 $refmol ./refmol.sdf && | |
10 python -m pipelines.rdkit.constrained_conf_gen | |
11 -i '$infile' | |
12 -if sdf | |
13 -r './refmol.sdf' | |
14 #if $core_smi | |
15 -c '$core_smi' | |
16 #end if | |
17 -n $number | |
18 --refmolidx $refmolidx | |
19 --meta | |
20 -o outp | |
21 -of sdf &>> $logfile && | |
22 cat outp_metrics.txt &>> $logfile && | |
23 gzip -dc outp.sdf.gz &>> outp.sdf || : | |
24 ]]></command> | |
25 <inputs> | |
26 <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/> | |
27 <param name="refmol" type="data" format="sdf" label="SDF reference file" help="ABCD"/> | |
28 <param name="refmolidx" type="integer" value="1" label="Reference molecule index" help="Index of the reference molecule index in the file, if not the first"/> | |
29 <param name="number" type="integer" value="10" label="Number of conformers" help="Number of conformers to generate, if None then input structures are assumed to already be 3D')"/> | |
30 <param name="core_smi" type="text" value="" label="Core substructure" help="If not specified - guessed using MCS"/> | |
31 </inputs> | |
32 | |
33 <expand macro="outputs" /> | |
34 | |
35 <tests> | |
36 <test> | |
37 <param name="infile" value="XChemReactionMaker1.sdf" ftype="sdf"/> | |
38 <param name="refmol" value="ref_mol.sdf" ftype="sdf"/> | |
39 <param name="number" value="2" /> | |
40 <output name="outfile" ftype="sdf" file="constrained_conf_gen_output1.sdf"/> | |
41 </test> | |
42 </tests> | |
43 <help><![CDATA[ | |
44 | |
45 .. class:: infomark | |
46 | |
47 **What this tool does** | |
48 | |
49 This tool generates constrained conformers for a set of input molecules, using the chemistry toolkit RDKit. | |
50 | |
51 ----- | |
52 | |
53 .. class:: infomark | |
54 | |
55 **Input** | |
56 | |
57 | - Molecules in `SDF format`_ | |
58 | - Reference molecule in SDF format. | |
59 | |
60 .. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file | |
61 | |
62 | |
63 ----- | |
64 | |
65 .. class:: infomark | |
66 | |
67 **Output** | |
68 | |
69 SD-file containing generated conformers. | |
70 | |
71 ]]></help> | |
72 <expand macro="citations" /> | |
73 </tool> |