Mercurial > repos > bgruening > ctb_im_constrained_conf_gen

comparison constrained_conf_gen.xml @ 0:9c5121dd2fd4 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 05:25:31 -0400
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-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>