Mercurial > repos > ufz > data_manager_dfast
diff data_manager/dfast.xml @ 0:a3ef2075f00e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dfast commit ceec7eb1afdcdebbbc145e7fe9fa5a38dafcd9b0
| author | ufz |
|---|---|
| date | Wed, 16 Apr 2025 10:58:35 +0000 |
| parents | |
| children | 23aec9361162 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/dfast.xml Wed Apr 16 10:58:35 2025 +0000 @@ -0,0 +1,56 @@ +<tool id="data_manager_dfast" name="DFAST data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01"> + <macros> + <token name="@TOOL_VERSION@">1.3.6</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">dfast</requirement> + </requirements> + <version_command>dfast --version | cut -d" " -f3</version_command> + <command detect_errors="exit_code"><![CDATA[ + mkdir '$output_file.extra_files_path' && + wget https://dfast.annotation.jp/dfast_core_db.tar.gz && + tar -xvf dfast_core_db.tar.gz && + mv db/* '$output_file.extra_files_path'/ && + cp '$dmjson' '$output_file' + ]]></command> + <configfiles> + <configfile name="dmjson"><![CDATA[ +#from datetime import datetime +#set version_id=datetime.now().strftime("%Y-%m-%d-%H%M%S") + { + "data_tables":{ + "dfast":[ + { + "value":"$version_id", + "description":"DFAST DB from $version_id", + "version":"$version_id", + "path":"$output_file.extra_files_path" + } + ] + } + }]]></configfile> + </configfiles> + <inputs> + <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/> + </inputs> + <outputs> + <data name="output_file" format="data_manager_json"/> + </outputs> + <tests> + <test> + <output name="output_file"> + <assert_contents> + <has_text text="DFAST DB"/> + <has_text text="dfast"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + This data managers fetches DFAST reference data from https://dfast.annotation.jp/ + ]]></help> + <citations> + <citation type="doi">10.5281/zenodo.4054262</citation> + </citations> +</tool>
