Mercurial > repos > bgruening > autodock_vina

comparison docking.xml @ 8:7a871df65202 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:13:41 -0400
parents 7b2f205b3f68
children 90ea16534012
comparison
equal deleted inserted replaced
7:7b2f205b3f68 8:7a871df65202
1 <tool id="docking" name="VINA Docking" version="0.3.0"> 1 <tool id="docking" name="VINA Docking" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <macros>
3 <token name="@TOOL_VERSION@">1.1.2</token>
4 <token name="@GALAXY_VERSION@">0</token>
5 </macros>
2 <description>tool to perform protein-ligand docking with Autodock Vina</description> 6 <description>tool to perform protein-ligand docking with Autodock Vina</description>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="1.1.2">autodock-vina</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">autodock-vina</requirement>
5 <requirement type="package" version="2.4.1">openbabel</requirement> 9 <requirement type="package" version="3.1.1">openbabel</requirement>
6 <requirement type="package" version="20190722">parallel</requirement> 10 <requirement type="package" version="20200722">parallel</requirement>
7 </requirements> 11 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
9 #if $ligands.is_of_type("sdf") 13 #if $ligands.is_of_type("sdf")
10 obabel -isdf '$ligands' -O ligand.pdbqt -m -p $ph_value && 14 obabel -isdf '$ligands' -O ligand.pdbqt -m -p $ph_value &&
11 #else 15 #else
95 <test> 99 <test>
96 <param name="receptor" value="protein.pdbqt"/> 100 <param name="receptor" value="protein.pdbqt"/>
97 <param name="ligands" value="input_ligand.pdbqt"/> 101 <param name="ligands" value="input_ligand.pdbqt"/>
98 <param name="box" value="box.txt"/> 102 <param name="box" value="box.txt"/>
99 <output_collection name="sdf_outputs" type="list" count="1"> 103 <output_collection name="sdf_outputs" type="list" count="1">
100 <element name="ligand1_docked" file="ligand1_docked.sdf" lines_diff="20"/> 104 <element name="ligand1_docked" file="ligand_docked.sdf" lines_diff="1084"/>
101 </output_collection> 105 </output_collection>
102 </test> 106 </test>
103 107
104 <!-- TODO - this should be able to use the same output as the previous test but there is inconsistency in 108 <!-- TODO - this should be able to use the same output as the previous test but there is inconsistency in
105 how the parameters are handled that needs to be resolved so we use a different output file to compare to. --> 109 how the parameters are handled that needs to be resolved so we use a different output file to compare to. -->
112 <param name="center_z" value="75.176" /> 116 <param name="center_z" value="75.176" />
113 <param name="size_x" value="18.768" /> 117 <param name="size_x" value="18.768" />
114 <param name="size_y" value="10.205999999999996" /> 118 <param name="size_y" value="10.205999999999996" />
115 <param name="size_z" value="15.521999999999991" /> 119 <param name="size_z" value="15.521999999999991" />
116 <param name="seed" value="true" /> 120 <param name="seed" value="true" />
117 <param name="seed_value" value="1" /> 121 <param name="seed_value" value="8" />
118 <param name="exh" value="10" /> 122 <param name="exh" value="10" />
119 <output_collection name="sdf_outputs" type="list" count="1"> 123 <output_collection name="sdf_outputs" type="list" count="1">
120 <element name="ligand1_docked" file="ligand_params.sdf" lines_diff="20"/> 124 <element name="ligand1_docked" file="ligand_params.sdf" lines_diff="1084"/>
121 </output_collection> 125 </output_collection>
122 </test> 126 </test>
123 127
124 </tests> 128 </tests>
125 <help><![CDATA[ 129 <help><![CDATA[