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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
author bgruening
date Wed, 22 May 2019 07:42:51 -0400
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deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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1 <tool id="get_pdb" name="Get PDB file" version="0.1.0">
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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2 <description>from Protein Data Bank</description>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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3 <requirements>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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4 <requirement type="package" version="1.20.1">wget</requirement>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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5 </requirements>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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6 <command detect_errors="exit_code"><![CDATA[
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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7 wget https://files.rcsb.org/download/${pdb_id}.pdb -O '$output'
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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8 ]]></command>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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9 <inputs>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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10 <param name="pdb_id" type="text" label="PDB accession code">
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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11 <validator type="regex" message="Invalid accession code">^[0-9][a-zA-Z0-9]{3}$</validator>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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12 </param>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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13 </inputs>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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14 <outputs>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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15 <data name="output" format="pdb" />
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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16 </outputs>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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17 <tests>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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18 <test>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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19 <param name="pdb_id" value="1AKI"/>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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20 <output name="output" file="1AKI.pdb"/>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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21 </test>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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22 </tests>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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23 <help><![CDATA[
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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24 Download a protein structure in PDB format from the Protein Data Bank using its four-letter accession code.
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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25 ]]></help>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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26 <citations>
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27 <citation type="doi">10.1093/nar/28.1.235</citation>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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28 </citations>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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29 </tool>