Mercurial > repos > pimarin > data_manager_bakta

annotate data_manager/bakta_build_database.xml @ 0:9d08486abf8e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
author pimarin
date Wed, 17 Aug 2022 14:42:22 +0000
parents
children faae5d8ce0cb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
1 <?xml version="1.0"?>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
2 <tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
3 <description> Bakta database builder </description>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
4 <macros>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
5 <import>macro.xml</import>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
6 </macros>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
7 <expand macro="requirements"/>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
8 <expand macro="version_command"/>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
9 <command detect_errors="aggressive"><![CDATA[
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
10 python '$__tool_directory__/bakta_build_database.py'
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
11 #if $database_command == "download"
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
12 download --output $output_file
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
13 #else if $database_command == "update"
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
14 #else if $database_command == "update"
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
15 update --db $output_file
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
16 #end if
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
17 ]]></command>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
18 <inputs>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
19 <conditional>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
20 <param name="database_command" type="select" label="Database action" multiple="false" help="Action on bakta database. Install or update database">
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
21 <option value="download"> Download a prebuild bakta database</option>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
22 <option value="custom"> Download a custom database</option>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
23 <option value="update"> Update the databases</option>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
24 </param>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
25 <when value="download"/>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
26 <when value="update"/>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
27 <when value="custom">
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
28 <param name="db_link"></param>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
29 </when>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
30 </conditional>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
31 </inputs>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
32 <outputs>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
33 <data name="output_file" format="data_manager_json" />
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
34 </outputs>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
35 <tests>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
36
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
37 <!-- TEST2 update -->
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
38 <test expect_num_outputs="1">
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
39 <param name="database_command" value="update"/>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
40 <output name="output_file">
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
41 <assert_contents>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
42 <has_text text="pangoLEARN data release 2021-04-01"/>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
43 <has_text text='"format_version": "1.0"'/>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
44 </assert_contents>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
45 </output>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
46 </test>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
47 </tests>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
48 <help><![CDATA[
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
49 Download, update or list bakta databases <https://github.com/oschwengers/bakta#database>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
50 ]]></help>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
51 <citations>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
52 <citation type="doi">10.1099/mgen.0.000685</citation>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
53 </citations>
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
diff changeset
54 </tool>