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busco DM: consider odb version
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recently odb12 became available for prokaryotes.
download would now mix now odb10 and 12.
see https://gitlab.com/ezlab/busco/-/issues/784

we unfortunately have no version column .. but having
it in the name and label might be OK
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bernt-matthias committed Feb 27, 2025
1 parent c6d65d9 commit a75ec90
Showing 1 changed file with 15 additions and 5 deletions.
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<description>dataset dowloader</description>
<macros>
<token name="@TOOL_VERSION@">5.8.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>
</macros>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">busco</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
mkdir '$out_file.extra_files_path' &&
busco --download_path '$out_file.extra_files_path' --download '$lineage' &&
## moving first to tmp folder until --datasets_version works
## https://gitlab.com/ezlab/busco/-/issues/784
mkdir tmp &&
busco --download_path tmp/ --download '$lineage' &&
mv -r tmp/*$dataset_version* '$out_file.extra_files_path'/
find '$out_file.extra_files_path' ! -name ""
cp '$dmjson' '$out_file'
]]></command>
<configfiles>
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"data_tables":{
"busco_database":[
{
"value":"$lineage #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
"name":"$lineage #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
"value":"$lineage $datasets_version #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
"name":"$lineage $datasets_version #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
"version":"@TOOL_VERSION@",
"path":"$out_file.extra_files_path"
}
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</configfile>
</configfiles>
<inputs>
<param name="lineage" type="select" label="Select the lineage to be downloaded">
<param name="lineage" argument="--download" type="select" label="Select the lineage to be downloaded">
<option value="all">All</option>
<option value="prokaryota">Prokaryota</option>
<option value="eukaryota">Eukaryota</option>
<option value="virus">Virus</option>
</param>
<param argument="--datasets_version" type="select" label="OrthoDB version">
<option value="odb10" selected="true">OrthoDB 10</option>
<option value="odb12">OrthoDB 12</option>
</param>
</inputs>
<outputs>
<data name="out_file" format="data_manager_json" label="BUSCO data manager: JSON"/>
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