Mercurial > repos > card > rgi

annotate data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.xml @ 2:a671367c326e draft

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"planemo upload for repository https://github.com/arpcard/rgi commit 481838067117d0c8ae84bc92ee58f47cfc18aa5f"
author card
date Tue, 17 Nov 2020 00:23:36 +0000
parents f96cbb663aa9
children bfbfc24c5af2
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715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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1 <?xml version="1.0"?>
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a671367c326e "planemo upload for repository https://github.com/arpcard/rgi commit 481838067117d0c8ae84bc92ee58f47cfc18aa5f"
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2 <tool id="rgi_database_builder" name="RGI Database Builder" tool_type="manage_data" version="1.1.0">
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3 <description>Download and build the CARD database for RGI</description>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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4 <requirements>
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a671367c326e "planemo upload for repository https://github.com/arpcard/rgi commit 481838067117d0c8ae84bc92ee58f47cfc18aa5f"
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5 <requirement type="package" version="5.1.1">rgi</requirement>
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715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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6 </requirements>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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7 <stdio>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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8 <exit_code description="Error" level="fatal" range="1:" />
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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9 </stdio>
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10 <command>
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11 <![CDATA[
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a671367c326e "planemo upload for repository https://github.com/arpcard/rgi commit 481838067117d0c8ae84bc92ee58f47cfc18aa5f"
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12 python3 rgi_database_builder.py --out "${out_file}"
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715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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13 #if $name:
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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14 --name "${name}"
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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15 #end if
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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16 #if $url:
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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17 --url "${url}"
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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18 #end if
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="name" type="text" value="" label="Database name" help="Name for this database, or leave blank for today's date" optional="True"/>
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23 <param name="url" type="text" value="https://card.mcmaster.ca/latest/data" label="Url" help="Url for the CARD data e.g https://card.mcmaster.ca/lastest/data. Visit https://card.mcmaster.ca/download to see previous CARD releases." optional="True"/>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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24 </inputs>
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25 <outputs>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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26 <data format="data_manager_json" name="out_file" label="${tool.name} (JSON)"/>
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27 </outputs>
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28 </tool>