Mercurial > repos > card > rgi
annotate data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.xml @ 3:bfbfc24c5af2 draft
"planemo upload for repository https://github.com/arpcard/rgi commit 101f923fe5bb3fb80716adb5320b96cef8ae2386"
author | card |
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date | Fri, 20 Nov 2020 18:57:39 +0000 |
parents | a671367c326e |
children | ce852ee2c394 |
rev | line source |
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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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715bc9aeef69
planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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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
card
parents:
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9 </stdio> |
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a671367c326e
"planemo upload for repository https://github.com/arpcard/rgi commit 481838067117d0c8ae84bc92ee58f47cfc18aa5f"
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10 <command> |
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715bc9aeef69
planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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11 <![CDATA[ |
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"planemo upload for repository https://github.com/arpcard/rgi commit 101f923fe5bb3fb80716adb5320b96cef8ae2386"
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12 python3 '$__tool_directory__/rgi_database_builder.py' --out "${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 ]]> |
715bc9aeef69
planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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20 </command> |
715bc9aeef69
planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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21 <inputs> |
715bc9aeef69
planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
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parents:
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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"/> |
715bc9aeef69
planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
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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
card
parents:
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24 </inputs> |
715bc9aeef69
planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
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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)"/> |
715bc9aeef69
planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
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27 </outputs> |
715bc9aeef69
planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
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28 </tool> |