Mercurial > repos > bgruening > autodock_vina

annotate docking.xml @ 12:25dd0fc20801 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/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
author bgruening
date Tue, 21 Dec 2021 14:18:05 +0000
parents fed21d976a4d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
fed21d976a4d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 10
diff changeset
1 <tool id="docking" name="VINA Docking" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
2 <description>tool to perform protein-ligand docking with Autodock Vina</description>
11
fed21d976a4d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 10
diff changeset
3 <macros>
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
4 <token name="@TOOL_VERSION@">1.2.3</token>
11
fed21d976a4d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 10
diff changeset
5 <token name="@GALAXY_VERSION@">0</token>
fed21d976a4d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 10
diff changeset
6 </macros>
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
7 <requirements>
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">vina</requirement>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
9 <requirement type="package" version="3.9">python</requirement>
11
fed21d976a4d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 10
diff changeset
10 <requirement type="package" version="3.1.1">openbabel</requirement>
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
11 <requirement type="package" version="20211022">parallel</requirement>
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
12 </requirements>
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
13 <command detect_errors="exit_code"><![CDATA[
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
14 #if $ligands.is_of_type("sdf")
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
15 obabel -isdf '$ligands' -O ligand.pdbqt -m -p $ph_value &&
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
16 #else
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
17 ln -s '$ligands' ligand1.pdbqt &&
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
18 #end if
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
19 mkdir output &&
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
20 ls ligand*.pdbqt | parallel --will-cite -j \${GALAXY_SLOTS:-1} $'OUTNAME={.}_docked && vina
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
21 --receptor \'$receptor\'
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
22 #if $flex:
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
23 --flex \'$flex\'
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
24 #end if
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
25 --ligand {}
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
26 --out ./\${OUTNAME}.pdbqt
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
27 --cpu 1
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
28 --verbosity 2
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
29 #if $config_params.config_params == "vals":
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
30 --center_x $config_params.center_x
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
31 --center_y $config_params.center_y
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
32 --center_z $config_params.center_z
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
33 --size_x $config_params.size_x
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
34 --size_y $config_params.size_y
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
35 --size_z $config_params.size_z
9
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
36 #if $config_params.exh != "":
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
37 --exhaustiveness $config_params.exh
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
38 #end if
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
39 #if $config_params.seed.seed == "true":
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
40 --seed $config_params.seed.seed_value
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
41 #end if
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
42 #else if $config_params.config_params == "file":
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
43 --config $config_params.box
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
44 #if $config_params.exh != "":
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
45 --exhaustiveness $config_params.exh
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
46 #end if
9
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
47 #end if
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
48 #if $settings.scoring:
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
49 --scoring \'$settings.scoring\'
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
50 #end if
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
51 #if $settings.num_modes:
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
52 --num_modes \'$settings.num_modes\'
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
53 #end if
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
54 #if $settings.min_rmsd:
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
55 --min_rmsd \'$settings.min_rmsd\'
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
56 #end if
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
57 #if $settings.energy_range:
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
58 --energy_range \'$settings.energy_range\'
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
59 #end if
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
60 #if $output == "sdf":
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
61 && python \'$__tool_directory__/convert_pdbqt_to_sdf.py\' ./\${OUTNAME}.pdbqt output/\${OUTNAME}.sdf
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
62 #end if
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
63 '
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
64 #if $output == "pdbqt":
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
65 && mv *docked.pdbqt output/
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
66 #end if
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
67 ]]></command>
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
68 <inputs>
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
69 <param type="data" name="receptor" format="pdbqt" label="Receptor" help="Select a receptor (PDBQT format). This can be prepared using the receptor preparation tool. If the 'Flexible side chains' option is chosen, it should contain only the rigid part of the receptor." />
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
70 <param type="data" name="ligands" format="sdf,pdbqt" label="Ligands" help="Select ligands (SDF format with multiple ligands or PDBQT format with single ligand)." />
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
71 <param type="data" name="flex" format="pdbqt" optional="true" label="Flexible side chains" help="Part of the receptor which should be treated flexibly (PDBQT format)." />
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
72 <param name="ph_value" type="float" value="7.4" min="0" max="14" label="Specify pH value for ligand protonation"
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
73 help="Only used if the input is a SD file."/>
8
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
74 <conditional name="config_params">
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
75 <param name="config_params" type="select" label="Specify parameters">
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
76 <option value="file">Upload a config file to specify parameters</option>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
77 <option value="vals">Specify values directly</option>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
78 </param>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
79 <when value="vals">
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
80 <param type="float" name="center_x" label="x coordinate" help="x coordinate of the binding site." value="0"/>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
81 <param type="float" name="center_y" label="y coordinate" help="y coordinate of the binding site." value="0"/>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
82 <param type="float" name="center_z" label="z coordinate" help="z coordinate of the binding site." value="0"/>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
83 <param type="float" name="size_x" label="x size" help="Length of the binding site (Å) in the x direction." value="0"/>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
84 <param type="float" name="size_y" label="y size" help="Length of the binding site (Å) in the y direction." value="0"/>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
85 <param type="float" name="size_z" label="z size" help="Length of the binding site (Å) in the z direction." value="0"/>
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
86 <param type="integer" name="exh" label="Exhaustiveness" optional="true"
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
87 help="Exhaustiveness of global search (optional - if not specified a default of 8 is used)"/>
8
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
88 <conditional name="seed">
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
89 <param name="seed" type="boolean" label="Specify random seed for simulation reproducibility?"/>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
90 <when value="true">
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
91 <param type="integer" name="seed_value" label="Random seed" help="Choose a seed value" value="1"/>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
92 </when>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
93 <when value="false"/>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
94 </conditional>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
95 </when>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
96 <when value="file">
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
97 <param type="data" name="box" format="txt" label="Box configuration" help="Text file with the box configurations" />
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
98 <param type="integer" name="exh" label="Exhaustiveness" optional="true"
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
99 help="Exhaustiveness of global search (optional - if not specified a default of 8 is used, if specified will override any value specified in the config file)"/>
8
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
100 </when>
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
101 </conditional>
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
102
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
103 <section name="settings" title="Optional settings" expanded="true" help="All these settings can also be specified in the config file. Specifying them additionally here overrides the config file.">
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
104 <param type="select" name="scoring" label="Scoring function" optional="true" help="Function to use for scoring the poses." value="vina">
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
105 <option value="vina">vina</option>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
106 <option value="ad4">ad4</option>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
107 <option value="vinardo">vinardo</option>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
108 </param>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
109 <param type="integer" name="num_modes" optional="true" label="Number of poses" help="Maximum number of binding poses to generate (default 9)" />
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
110 <param type="float" name="min_rmsd" optional="true" label="Minimum RMSD between output poses (default 1)" />
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
111 <param type="float" name="energy_range" optional="true" label="Energy range" help="Maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) (default 3)"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
112 </section>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
113 <param type="select" name="output" label="Output format" help="Format for the docking poses.">
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
114 <option value="sdf" selected="true">SDF</option>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
115 <option value="pdbqt">PDBQT</option>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
116 </param>
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
117 </inputs>
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
118 <outputs>
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
119 <collection name="sdf_outputs" type="list" label="Docked ligands for ${on_string}" >
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
120 <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" />
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
121 <filter>output == "sdf"</filter>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
122 </collection>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
123 <collection name="pdbqt_outputs" type="list" label="Docked structures for ${on_string}" >
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
124 <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" />
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
125 <filter>output == "pdbqt"</filter>
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
126 </collection>
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
127 </outputs>
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
128 <tests>
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
129 <test>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
130 <param name="receptor" value="protein.pdbqt"/>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
131 <param name="ligands" value="input_ligands.sdf"/>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
132 <param name="box" value="box.txt"/>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
133 <output_collection name="sdf_outputs" type="list" count="5">
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
134 <!-- linesdiff because there is a time stamp for each of the 9 poses -->
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
135 <element name="ligand1_docked" file="ligand1_docked.sdf" lines_diff="18"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
136 <element name="ligand2_docked" file="ligand2_docked.sdf" lines_diff="18"/>
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
137 <!-- we check only the first 2 -->
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
138 </output_collection>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
139 </test>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
140
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
141 <test>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
142 <param name="receptor" value="protein.pdbqt"/>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
143 <param name="ligands" value="input_ligand.pdbqt"/>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
144 <param name="box" value="box.txt"/>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
145 <output_collection name="sdf_outputs" type="list" count="1">
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
146 <element name="ligand1_docked" file="ligand_docked.sdf" lines_diff="18"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
147 </output_collection>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
148 </test>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
149
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
150 <!-- test with optional params -->
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
151 <test>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
152 <param name="receptor" value="protein.pdbqt"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
153 <param name="ligands" value="input_ligand.pdbqt"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
154 <param name="box" value="box.txt"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
155 <param name="scoring" value="vinardo"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
156 <param name="energy_range" value="5"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
157 <param name="num_modes" value="20"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
158 <param name="min_rmsd" value="0.5"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
159 <output_collection name="sdf_outputs" type="list" count="1">
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
160 <element name="ligand1_docked" file="ligand_docked_opt.sdf" lines_diff="40"/>
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
161 </output_collection>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
162 </test>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
163
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
164 <!-- TODO - this should be able to use the same output as the previous test but there is inconsistency in
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
165 how the parameters are handled that needs to be resolved so we use a different output file to compare to. -->
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
166 <test>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
167 <param name="receptor" value="protein.pdbqt"/>
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
168 <param name="ligands" value="input_ligand.pdbqt"/>
8
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
169 <param name="config_params" value="vals"/>
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
170 <param name="center_x" value="36.454" />
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
171 <param name="center_y" value="-43.608000000000004" />
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
172 <param name="center_z" value="75.176" />
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
173 <param name="size_x" value="18.768" />
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
174 <param name="size_y" value="10.205999999999996" />
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
175 <param name="size_z" value="15.521999999999991" />
8
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
176 <param name="seed" value="true" />
11
fed21d976a4d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 10
diff changeset
177 <param name="seed_value" value="8" />
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
178 <param name="exh" value="10" />
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
179 <output_collection name="sdf_outputs" type="list" count="1">
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
180 <element name="ligand1_docked" file="ligand_params.sdf" lines_diff="18"/>
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
181 </output_collection>
8
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
182 </test>
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
183
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
184 <!-- flexible docking -->
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
185 <test>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
186 <param name="receptor" value="protein_rigid.pdbqt"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
187 <param name="flex" value="protein_flex.pdbqt"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
188 <param name="ligands" value="input_ligands.sdf"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
189 <param name="config_params" value="vals"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
190 <param name="center_x" value="15.2" />
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
191 <param name="center_y" value="53.9" />
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
192 <param name="center_z" value="16.9" />
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
193 <param name="size_x" value="20" />
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
194 <param name="size_y" value="20" />
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
195 <param name="size_z" value="20" />
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
196 <param name="seed" value="true" />
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
197 <param name="seed_value" value="8" />
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
198 <param name="exh" value="10" />
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
199 <param name="output" value="pdbqt"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
200 <output_collection name="pdbqt_outputs" type="list" count="5">
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
201 <element name="ligand1_docked" file="ligand1_docked_flex.pdbqt"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
202 <element name="ligand2_docked" file="ligand2_docked_flex.pdbqt"/>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
203 <!-- we check only the first 2 -->
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
204 </output_collection>
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
205 </test>
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
206 </tests>
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
207 <help><![CDATA[
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
208
8
351c0b372682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 7
diff changeset
209 This tool performs protein-ligand docking using the Autodock Vina program.
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
210
9
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
211 -----
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
212
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
213 .. class:: infomark
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
214
7
5327811c2835 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 6
diff changeset
215 **Inputs**
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
216
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
217 The first two inputs required are files describing the receptor (in the pdbqt format) and ligands (in SDF of PDBQT format) respectively.
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
218 These files are produced by the receptor and ligand preparation tools.
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
219 If using PDBQT format for the ligands only a single ligand can be specified. If using SDF you can include multiple ligands
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
220 and those ligands are converted to individual PDBQT format files using openbabel as the first step of tool execution.
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
221 You can specify the pH for protonation by openbabel
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
222
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
223 VINA will dock each of the ligands in the SDF file sequentially. If there are a large number of ligands then first split
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
224 them into a collection of smaller files e.g. using the splitter tool. This allows each split chunk of molecules to be docked
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
225 as a separate task. The optimal size of the chunk will depend on the number of ligands and the capacity of the execution
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
226 environment.
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
227
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
228 In addition, parameters for docking must be defined. The Cartesian coordinates of the center of the binding site should
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
229 be provided, along with the size of the binding site along each dimension. Effectively, this defines a cuboidal volume in
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
230 which docking is performed. Alternatively, a config file can be uploaded containing this information - such a file can be
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
231 generated from the box parameter calculation file.
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
232
9
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
233
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
234 -----
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
235
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
236 .. class:: infomark
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
237
7
5327811c2835 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
bgruening
parents: 6
diff changeset
238 **Outputs**
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
239
10
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
240 SDF files are produced as output.
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
241 There is one file for each ligand in the input. Each entry in the file is a docked pose for that ligand.
9bff7ae75b03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 9
diff changeset
242 The binding affinity scores are contained within the SDF file.::
9
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
243
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
244 OpenBabel06171915303D
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
245
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
246 23 23 0 0 0 0 0 0 0 0999 V2000
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
247 66.9030 73.3450 36.0040 O 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
248 66.8190 73.2170 37.2120 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
249 66.0490 72.3370 37.8940 O 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
250 66.2290 70.9500 37.5970 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
251 67.2070 70.4140 38.6010 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
252 68.5140 70.1440 38.3980 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
253 69.2150 70.3400 37.0800 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
254 69.3810 69.5970 39.5210 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
255 68.7730 69.8280 40.9100 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
256 69.3750 71.0120 41.6220 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
257 68.7550 72.1570 41.9760 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
258 67.3280 72.4970 41.6430 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
259 69.4770 73.2270 42.7560 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
260 67.5570 74.0540 38.1920 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
261 66.9010 75.0480 38.9340 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
262 67.6300 75.8170 39.8300 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
263 68.9950 75.5990 39.9980 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
264 69.6510 74.6060 39.2850 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
265 68.9300 73.8240 38.3800 C 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
266 67.0450 76.8040 40.5760 O 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
267 67.5560 77.4980 40.9760 H 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
268 69.7010 76.3670 40.8780 O 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
269 69.2520 76.7930 41.5990 H 0 0 0 0 0 0 0 0 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
270 1 2 2 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
271 2 3 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
272 2 14 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
273 4 3 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
274 4 5 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
275 6 5 2 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
276 6 8 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
277 7 6 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
278 8 9 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
279 9 10 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
280 10 11 2 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
281 11 13 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
282 12 11 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
283 14 19 2 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
284 14 15 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
285 15 16 2 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
286 16 17 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
287 16 20 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
288 17 22 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
289 18 17 2 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
290 19 18 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
291 20 21 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
292 22 23 1 0 0 0 0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
293 M END
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
294 > <MODEL>
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
295 1
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
296
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
297 > <REMARK>
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
298 VINA RESULT: 0.0 0.000 0.000
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
299 9 active torsions:
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
300 status: ('A' for Active; 'I' for Inactive)
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
301 1 A between atoms: C_2 and O_3
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
302 2 A between atoms: C_2 and C_14
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
303 3 A between atoms: O_3 and C_4
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
304 4 A between atoms: C_4 and C_5
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
305 5 A between atoms: C_6 and C_8
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
306 6 A between atoms: C_8 and C_9
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
307 7 A between atoms: C_9 and C_10
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
308 8 A between atoms: C_16 and O_17
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
309 9 A between atoms: C_19 and O_20
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
310
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
311 > <TORSDO>
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
312 F 9
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
313
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
314 > <SCORE>
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
315 0.0
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
316
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
317 > <RMSD_LB>
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
318 0.000
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
319
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
320 > <RMSD_UB>
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
321 0.000
bbba4373ddc2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 8
diff changeset
322
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
323 ]]></help>
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
324 <citations>
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
325 <citation type="doi">10.1002/jcc.21334</citation>
12
25dd0fc20801 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 11
diff changeset
326 <citation type="doi">10.1021/acs.jcim.1c00203</citation>
6
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
327 </citations>
f0ddfdc80f8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 877e088cd0a2a33cd4d24378ad3ab48d86e3f95d
bgruening
parents:
diff changeset
328 </tool>