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comparison docking.xml @ 3:65ffed035ca8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
author bgruening
date Sat, 04 Jun 2016 12:36:59 -0400
parents 18dec59e29ae
children 3c8e86318a81
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2:18dec59e29ae 3:65ffed035ca8
1 <tool id="docking" name="Docking" version="0.1.0"> 1 <tool id="docking" name="Docking" version="0.1.0">
2 <description>- Tool to running molecular docking with Autodock Vina</description> 2 <description>Tool to running molecular docking with Autodock Vina</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.2">autodock-vina</requirement> 4 <requirement type="package" version="1.1.2">autodock-vina</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1" /> 7 <exit_code range="1" />
8 </stdio> 8 </stdio>
9 <command><![CDATA[ 9 <command><![CDATA[
10 vina --config "$box" --receptor "$receptor" --ligand "$ligand" --out "$file_output1" --log "$file_output2" 10 vina --config "$box" --receptor "$receptor" --ligand "$ligand" --out "$file_output1" --log "$file_output2"
11 ]]></command> 11 ]]></command>
12 <inputs> 12 <inputs>
13 <param type="data" name="box" format="txt" label="Box configuration: " help="Select a text file with the box configurations" /> 13 <param type="data" name="box" format="txt" label="Box configuration" help="Select a text file with the box configurations" />
14 <param type="data" name="receptor" format="pdbqt" label="Receptor: " help="Select a receptor pdbqt file" /> 14 <param type="data" name="receptor" format="pdbqt" label="Receptor" help="Select a receptor PDBQT format. This can be prepared using the receptor preparation tool." />
15 <param type="data" name="ligand" format="pdbqt" label="Ligand: " help="Select a ligand pdbqt file" /> 15 <param type="data" name="ligand" format="pdbqt" label="Ligand" help="Select a ligand PDBQT format. This can be prepared using the ligand preparation tool." />
16 </inputs> 16 </inputs>
17 <outputs> 17 <outputs>
18 <data name="file_output1" format="pdbqt" label="#echo (os.path.splitext (str($ligand.name))[0]) + '_-_' + (os.path.splitext (str($receptor.name))[0])#.pdbqt" /> 18 <data name="file_output1" format="pdbqt" />
19 <data name="file_output2" format="txt" label="#echo (os.path.splitext (str($ligand.name))[0]) + '_-_' + (os.path.splitext (str($receptor.name))[0])#.log" /> 19 <data name="file_output2" format="txt" />
20 </outputs> 20 </outputs>
21 <tests> 21 <tests>
22 <test> 22 <test>
23 <param name="box" value="config_complexo_dm.txt"/> 23 <param name="box" value="config_complexo_dm.txt"/>
24 <param name="receptor" value="3u1i_for_DM.pdbqt"/> 24 <param name="receptor" value="3u1i_for_DM.pdbqt"/>