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busco DM: consider odb version #6808

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busco DM: consider odb version #6808

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a75ec90
busco DM: consider odb version
bernt-matthias Feb 27, 2025
b7241b3
fix variable name
bernt-matthias Feb 27, 2025
f15c4d9
remove -r
bernt-matthias Feb 27, 2025
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20 changes: 15 additions & 5 deletions data_managers/data_manager_fetch_busco/data_manager/busco_fetcher.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,14 +2,20 @@
<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 tmp/*$datasets_version* '$out_file.extra_files_path'/

find '$out_file.extra_files_path' ! -name ""
cp '$dmjson' '$out_file'
]]></command>
<configfiles>
Expand All @@ -19,8 +25,8 @@
"data_tables":{
"busco_database":[
{
"value":"$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"
}
Expand All @@ -30,12 +36,16 @@
</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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