Mercurial > repos > iuc > mg_toolkit_original_metadata
diff original_metadata.xml @ 0:2eef3b6f1c84 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit commit d5891ffcc42b812f9e072b4c58abc5077e947db0
author | iuc |
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date | Tue, 16 Jul 2024 09:23:54 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/original_metadata.xml Tue Jul 16 09:23:54 2024 +0000 @@ -0,0 +1,69 @@ +<tool id="mg_toolkit_original_metadata" name="Metagenomics toolkit Original Metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>Download original metadata for a study</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creators" /> + <expand macro="biotools" /> + <expand macro="requirements" /> + <command><![CDATA[ + mkdir output_metadata && + mg-toolkit original_metadata -a ${accessions} && + mv *.csv output_metadata + ]]></command> + + <inputs> + <param name="accessions" type="text" label="Accessions" help="Study/project accessions (e.g., ERP001736 SRP000319)" optional="false"> + <validator type="regex" message="Accessions separated with white spaces">^([A-Za-z]{3,4}\d+)(\s[A-Za-z]{3,4}\d+)*$</validator> + </param> + </inputs> + <outputs> + <collection name="output_collection" type="list" label="Original metadata"> + <discover_datasets pattern="(?P<designation>.+).csv" directory="output_metadata" format="csv"/> + </collection> + </outputs> + <tests> + <test> + <param name="accessions" value="ERP001736 SRP000319" /> + <output_collection name="output_collection" type="list"> + <element name="ERP001736"> + <assert_contents> + <has_n_lines n="250" /> + <has_size size="185577" /> + </assert_contents> + </element> + <element name="SRP000319"> + <assert_contents> + <has_n_lines n="30" /> + <has_size size="2855" /> + </assert_contents> + </element> + </output_collection> + </test> + <test> + <param name="accessions" value="ERP001736" /> + <output_collection name="output_collection" type="list"> + <element name="ERP001736"> + <assert_contents> + <has_n_lines n="250" /> + <has_size size="185577" /> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <help> +<![CDATA[ +The mg-toolkit original-metadata tool is part of the EMG Toolkit provided by EBI Metagenomics. +This tool allows users to retrieve the original metadata associated with metagenomic studies and analyses. +It facilitates the extraction of detailed contextual information submitted by researchers, +aiding in the interpretation and further analysis of metagenomic data. + +License +------- +* `Apache-2.0 license <https://raw.githubusercontent.com/EBI-Metagenomics/emg-toolkit/master/LICENSE>`_ + +]]> + </help> + <expand macro="citations" /> +</tool>