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Fix and update the omamer DM #7828

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Fix and update the omamer DM #7828

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19bfc0e
fix and update the omamer DM
bernt-matthias Mar 24, 2026
b6c9fce
try curl
bernt-matthias Mar 26, 2026
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12 changes: 0 additions & 12 deletions data_managers/data_manager_omamer/data_manager/macros.xml
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86 changes: 0 additions & 86 deletions data_managers/data_manager_omamer/data_manager/omamer.py
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63 changes: 45 additions & 18 deletions data_managers/data_manager_omamer/data_manager/omamer.xml
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Original file line number Diff line number Diff line change
@@ -1,24 +1,48 @@
<tool id="data_manager_omamer" name="OMAmer data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
<macros>
<import>macros.xml</import>
</macros>
<tool id="data_manager_omamer" name="OMAmer data manager" version="2.0.3+galaxy0" tool_type="manage_data" profile="24.2">
<requirements>
<requirement type="package" version="1.25.0">wget</requirement>
</requirements>
<version_command></version_command>
<command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/omamer.py'
--name '$name'
--json '$output_file'
--version '@TOOL_VERSION@'
mkdir '$output_file.extra_files_path'/ &&
curl https://omabrowser.org/${name}.h5 -o '$output_file.extra_files_path/${name}.h5' &&
cp '$dmjson' '$output_file'
]]></command>
<configfiles>
<configfile name="dmjson"><![CDATA[#slurp
#set $version, $basename = str($name).split("/")
## handling of 'legacy' data (2.0.2 of the DM used different values which we keep here)
#if $version == "All.Jul2023"
#set $value = $basename + ".h5"
#else
#set $value = $basename.replace("/", '-')
#end if
{
"data_tables": {
"omamer": [
{
"name": "$version $basename",
"path": "${basename}.h5",
"value": "$value",
"version": "$version"
}
]
}
}
]]></configfile>
</configfiles>
<inputs>
<param name="output_dir" type="text" label="Output Directory" value=""/>
<param name="name" type="select" label="Database">
<option value="Primates_v2.0.0">Primates_v2.0.0</option>
<option value="Viridiplantae_v2.0.0">Viridiplantae_v2.0.0</option>
<option value="Metazoa_v2.0.0">Metazoa_v2.0.0</option>
<option value="LUCA_v0.2.5">LUCA_v0.2.5</option>
<option value="LUCA_v2.0.0">LUCA_v2.0.0</option>
<option value="Saccharomyceta">Saccharomyceta</option>
<option value="Homininae">Homininae</option>
<option value="All.Jul2024/LUCA">All.Jul2024 LUCA</option>
<option value="All.Jul2024/Primates">All.Jul2024 Primates (only for testing the DM???)</option>

<option value="All.Jul2023/Primates-v2.0.0">All.Jul2023 Primates_v2.0.0</option>
<option value="All.Jul2023/Viridiplantae-v2.0.0">All.Jul2023 Viridiplantae_v2.0.0</option>
<option value="All.Jul2023/Metazoa-v2.0.0">All.Jul2023 Metazoa_v2.0.0</option>
<option value="All.Jul2023/LUCA-v0.2.5">All.Jul2023 LUCA_v0.2.5</option>
<option value="All.Jul2023/LUCA-v2.0.0">All.Jul2023 LUCA_v2.0.0</option>
<option value="All.Jul2023/Saccharomyceta">All.Jul2023 Saccharomyceta</option>
<option value="All.Jul2023/Homininae">All.Jul2023 Homininae</option>
</param>
</inputs>

Expand All @@ -28,10 +52,13 @@

<tests>
<test>
<param name="output_dir" value="test_galaxy"/>
<param name="name" value="Primates_v2.0.0"/>
<param name="name" value="All.Jul2023/Primates-v2.0.0"/>
<output name="output_file" file="out.json"/>
</test>
<test>
<param name="name" value="All.Jul2024/Primates"/>
<output name="output_file" file="2024.json"/>
</test>
</tests>

<help><![CDATA[
Expand Down
12 changes: 12 additions & 0 deletions data_managers/data_manager_omamer/test-data/2024.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
{
"data_tables": {
"omamer": [
{
"name": "All.Jul2024 Primates",
"path": "Primates.h5",
"value": "Primates",
"version": "All.Jul2024"
}
]
}
}
6 changes: 3 additions & 3 deletions data_managers/data_manager_omamer/test-data/out.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,11 @@
"data_tables": {
"omamer": [
{
"name": "Primates-v2.0.0",
"name": "All.Jul2023 Primates-v2.0.0",
"path": "Primates-v2.0.0.h5",
"value": "Primates-v2.0.0.h5",
"version": "2.0.2"
"version": "All.Jul2023"
}
]
}
}
}
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