Mercurial > repos > bgruening > get_pdb
comparison get_pdb.xml @ 0:538790c6c21b draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pdb commit 678c8fe83eb51fb36538c0719fceb9a97999c10f
| author | bgruening |
|---|---|
| date | Fri, 31 May 2019 06:22:47 -0400 |
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| children |
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| -1:000000000000 | 0:538790c6c21b |
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| 1 <tool id="get_pdb" name="Get PDB file" version="0.1.0"> | |
| 2 <description>from Protein Data Bank</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.20.1">wget</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 wget https://files.rcsb.org/download/${pdb_id}.pdb -O '$output' | |
| 8 ]]></command> | |
| 9 <inputs> | |
| 10 <param name="pdb_id" type="text" label="PDB accession code"> | |
| 11 <validator type="regex" message="Invalid accession code">^[0-9][a-zA-Z0-9]{3}$</validator> | |
| 12 </param> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data name="output" format="pdb" /> | |
| 16 </outputs> | |
| 17 <tests> | |
| 18 <test> | |
| 19 <param name="pdb_id" value="1AKI"/> | |
| 20 <output name="output" file="1AKI.pdb"/> | |
| 21 </test> | |
| 22 </tests> | |
| 23 <help><![CDATA[ | |
| 24 Download a protein structure in PDB format from the Protein Data Bank using its four-letter accession code. | |
| 25 ]]></help> | |
| 26 <citations> | |
| 27 <citation type="doi">10.1093/nar/28.1.235</citation> | |
| 28 </citations> | |
| 29 </tool> |