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comparison openduck_chunk.xml @ 0:89c3bd4f50a3 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
author bgruening
date Thu, 16 Apr 2020 08:25:04 -0400
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-1:000000000000 0:89c3bd4f50a3
1 <tool id="openduck_chunk" name="OpenDUck chunk" version="@VERSION@">
2 <description>for dynamic undocking</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 cp '$ligand' ./ligand.sdf &&
9 duck_chunk
10 -p '$protein'
11 -l ./ligand.sdf
12 -c '$cutoff'
13 $ignore_buffers
14 ## -i is interaction, e.g. A_ASP_156_OD2
15 -i '${ia.chain_sel}'_'${ia.res_sel}'_'${ia.resid_sel}'_'${ia.atom_sel}'
16
17 #if $return_tar:
18 && tar -czf allfiles.tar.gz --exclude=allfiles.tar.gz *
19 #end if
20
21 ]]></command>
22 <inputs>
23 <param argument="protein" type="data" format='pdb' label="PDB file for apoprotein"/>
24 <param argument="ligand" type="data" format='sdf,mol' label="SDF/MOL file containing a single ligand"/>
25 <param argument="cutoff" type="float" min="0" value="5" label="Cutoff" help="Cutoff for chunk generation (in angstroms)" />
26 <param argument="ignore_buffers" type="select" label="Ignore buffers (solvent, ions etc.)?">
27 <option value="">Remove buffers</option>
28 <option value="-b">Leave buffers</option>
29 </param>
30 <expand macro="interaction_params" />
31 <expand macro="tar_param" />
32
33 </inputs>
34 <outputs>
35 <data name="chunk" format="pdb" from_work_dir="protein_out_prot.pdb" label="${tool.name} PDB file"/>
36 <expand macro="tar_output" />
37 </outputs>
38 <tests>
39 <test expect_num_outputs="1">
40 <param name="protein" value="1n2v_apo.pdb" />
41 <param name="ligand" value="ligand.mol" />
42 <param name="cutoff" value="5" />
43 <param name="ignore_buffers" value="" />
44 <param name="chain_sel" value="A" />
45 <param name="res_sel" value="ASP" />
46 <param name="resid_sel" value="156" />
47 <param name="atom_sel" value="OD2" />
48 <param name="return_tar" value="false" />
49 <output name="chunk" file="protein_out_prot.pdb" />
50 </test>
51 </tests>
52 <help><![CDATA[
53
54 .. class:: infomark
55
56 **What it does**
57
58 Produce chunk automatically for dynamic undocking (DUck). Chunking entails selecting a region of the protein which is used for a DUck simulation.
59
60 This Galaxy tool uses OpenDUck, an open-source implementation of the original DUck method, using OpenMM and AmberTools.
61
62 _____
63
64 .. class:: infomark
65
66 **Input**
67
68 - PDB file for protein
69 - SDF/MOL file for ligand
70 - Parameters defining the protein-ligand interaction
71
72 _____
73
74
75 .. class:: infomark
76
77 **Output**
78
79 - PDB file containing the chunked protein ready for system preparation.
80
81 A tar file is also produced as a optional output, containing all files produced by the tool.
82
83 ]]></help>
84 <expand macro="citations" />
85 </tool>