Mercurial > repos > wolma > data_manager_packaged_annotation_data
comparison data_manager/install_packaged_annotation_data.xml @ 0:632d33df6758 draft
"planemo upload commit 3dc5291eccd1fb516be67694c18a27bda5f69f91"
author | wolma |
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date | Thu, 16 Dec 2021 18:26:23 +0000 |
parents | |
children | eb47f11e34fc |
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1 <tool id="data_manager_packaged_annotation_data" name="Download and install packaged collections of genome annotation data" version="0.0.1" tool_type="manage_data" profile="19.01"> | |
2 <description>fetching</description> | |
3 <requirements> | |
4 <requirement type="package" version="3.7">python</requirement> | |
5 <requirement type="package" version="5.1.1">pyyaml</requirement> | |
6 </requirements> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 python '$__tool_directory__/install_packaged_annotation_data.py' | |
9 --target-directory '${out_file.extra_files_path}' | |
10 -o '$out_file' | |
11 --dbkey '$dbkey' | |
12 '$metadata' | |
13 ]]></command> | |
14 <inputs> | |
15 <param name="dbkey" type="genomebuild" | |
16 label="DBKEY of genome that the annotation data is for" | |
17 help="Take a look at the refgenome value from the metadata file to guide you in your selection." /> | |
18 <param name="metadata" type="data" format="txt" label="Metadata describing the package and its contents" /> | |
19 </inputs> | |
20 <outputs> | |
21 <data name="out_file" format="data_manager_json" /> | |
22 </outputs> | |
23 <tests> | |
24 <!-- TODO: need some way to test that new entry was added to data table --> | |
25 <test> | |
26 <param name="dbkey" value="hg19"/> | |
27 <param name="metadata" value="test-meta.yml"/> | |
28 <output name="out_file" file="from_test-meta.data_manager.json"/> | |
29 </test> | |
30 </tests> | |
31 <help> | |
32 **What it does** | |
33 | |
34 This tool fetches and installs packages of genome annotation datasets that are | |
35 not tightly bound to specific tools, but generic enough to be of use for many different tools. | |
36 | |
37 It populates the "packaged_annotation_data" data table. | |
38 </help> | |
39 </tool> |