Mercurial > repos > rnateam > openduck_chunk

annotate openduck_chunk.xml @ 0:a7520d5c81e2 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/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
author rnateam
date Thu, 16 Apr 2020 12:13:18 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
1 <tool id="openduck_chunk" name="OpenDUck chunk" version="@VERSION@">
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
2 <description>for dynamic undocking</description>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
3 <macros>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
4 <import>macros.xml</import>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
5 </macros>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
6 <expand macro="requirements" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
8 cp '$ligand' ./ligand.sdf &&
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
9 duck_chunk
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
10 -p '$protein'
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
11 -l ./ligand.sdf
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
12 -c '$cutoff'
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
13 $ignore_buffers
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
14 ## -i is interaction, e.g. A_ASP_156_OD2
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
15 -i '${ia.chain_sel}'_'${ia.res_sel}'_'${ia.resid_sel}'_'${ia.atom_sel}'
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
16
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
17 #if $return_tar:
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
18 && tar -czf allfiles.tar.gz --exclude=allfiles.tar.gz *
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
19 #end if
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
20
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
21 ]]></command>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
22 <inputs>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
23 <param argument="protein" type="data" format='pdb' label="PDB file for apoprotein"/>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
24 <param argument="ligand" type="data" format='sdf,mol' label="SDF/MOL file containing a single ligand"/>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
25 <param argument="cutoff" type="float" min="0" value="5" label="Cutoff" help="Cutoff for chunk generation (in angstroms)" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
26 <param argument="ignore_buffers" type="select" label="Ignore buffers (solvent, ions etc.)?">
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
27 <option value="">Remove buffers</option>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
28 <option value="-b">Leave buffers</option>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
29 </param>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
30 <expand macro="interaction_params" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
31 <expand macro="tar_param" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
32
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
33 </inputs>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
34 <outputs>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
35 <data name="chunk" format="pdb" from_work_dir="protein_out_prot.pdb" label="${tool.name} PDB file"/>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
36 <expand macro="tar_output" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
37 </outputs>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
38 <tests>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
39 <test expect_num_outputs="1">
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
40 <param name="protein" value="1n2v_apo.pdb" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
41 <param name="ligand" value="ligand.mol" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
42 <param name="cutoff" value="5" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
43 <param name="ignore_buffers" value="" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
44 <param name="chain_sel" value="A" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
45 <param name="res_sel" value="ASP" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
46 <param name="resid_sel" value="156" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
47 <param name="atom_sel" value="OD2" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
48 <param name="return_tar" value="false" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
49 <output name="chunk" file="protein_out_prot.pdb" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
50 </test>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
51 </tests>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
52 <help><![CDATA[
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
53
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
54 .. class:: infomark
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
55
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
56 **What it does**
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
57
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
58 Produce chunk automatically for dynamic undocking (DUck). Chunking entails selecting a region of the protein which is used for a DUck simulation.
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
59
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
60 This Galaxy tool uses OpenDUck, an open-source implementation of the original DUck method, using OpenMM and AmberTools.
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
61
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
62 _____
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
63
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
64 .. class:: infomark
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
65
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
66 **Input**
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
67
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
68 - PDB file for protein
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
69 - SDF/MOL file for ligand
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
70 - Parameters defining the protein-ligand interaction
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
71
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
72 _____
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
73
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
74
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
75 .. class:: infomark
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
76
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
77 **Output**
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
78
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
79 - PDB file containing the chunked protein ready for system preparation.
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
80
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
81 A tar file is also produced as a optional output, containing all files produced by the tool.
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
82
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
83 ]]></help>
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
84 <expand macro="citations" />
a7520d5c81e2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"
rnateam
parents:
diff changeset
85 </tool>