Mercurial > repos > bgruening > autodock_vina
comparison docking.xml @ 3:65ffed035ca8 draft
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 |
comparison
equal
deleted
inserted
replaced
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"/> |