Mercurial > repos > card > rgi

annotate data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.xml @ 5:84bd24ac33fd draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/arpcard/rgi commit a87febbe1a31eb5b9918b18bc04097fe47766e71
author card
date Wed, 07 Sep 2022 13:05:05 +0000
parents ce852ee2c394
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
1 <?xml version="1.0"?>
5
84bd24ac33fd planemo upload for repository https://github.com/arpcard/rgi commit a87febbe1a31eb5b9918b18bc04097fe47766e71
card
parents: 4
diff changeset
2 <tool id="rgi_database_builder" name="RGI Database Builder" profile="18.09" tool_type="manage_data" version="1.2.0">
0
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
3 <description>Download and build the CARD database for RGI</description>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
4 <requirements>
4
ce852ee2c394 planemo upload for repository https://github.com/arpcard/rgi commit 78185f967f4c08824f0b118214adcecc14495f3e
card
parents: 3
diff changeset
5 <requirement type="package" version="5.2.1">rgi</requirement>
0
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
6 </requirements>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
7 <stdio>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
8 <exit_code description="Error" level="fatal" range="1:" />
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
9 </stdio>
2
a671367c326e "planemo upload for repository https://github.com/arpcard/rgi commit 481838067117d0c8ae84bc92ee58f47cfc18aa5f"
card
parents: 1
diff changeset
10 <command>
0
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
11 <![CDATA[
3
bfbfc24c5af2 "planemo upload for repository https://github.com/arpcard/rgi commit 101f923fe5bb3fb80716adb5320b96cef8ae2386"
card
parents: 2
diff changeset
12 python3 '$__tool_directory__/rgi_database_builder.py' --out "${out_file}"
0
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
13 #if $name:
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
14 --name "${name}"
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
15 #end if
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
16 #if $url:
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
17 --url "${url}"
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
18 #end if
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
19 ]]>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
20 </command>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
21 <inputs>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
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:
diff changeset
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:
diff changeset
24 </inputs>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
25 <outputs>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
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:
diff changeset
27 </outputs>
715bc9aeef69 planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
card
parents:
diff changeset
28 </tool>