Mercurial > repos > wolma > data_manager_packaged_annotation_data

annotate data_manager/install_packaged_annotation_data.xml @ 0:632d33df6758 draft

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