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Add mg-toolkit original_metadata (galaxyproject#6142)
* add mg-toolkit original_metadata * add citation * rename metadata.xml --> original_metadata.xml * add license * rename repo * minor adjustments & input validator * accession --> accessions * Update tools/mg_toolkit/original_metadata.xml * Apply suggestions from code review * update command * Update tools/mg_toolkit/original_metadata.xml --------- Co-authored-by: Björn Grüning <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| name: mg_toolkit | ||
| owner: iuc | ||
| description: Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. | ||
| homepage_url: https://github.com/EBI-Metagenomics/emg-toolkit | ||
| long_description: | | ||
| Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg-toolkit | ||
| categories: | ||
| - Metagenomics |
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| <macros> | ||
| <token name="@TOOL_VERSION@">0.10.4</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <xml name="requirements"> | ||
| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">mg-toolkit</requirement> | ||
| </requirements> | ||
| </xml> | ||
| <xml name="biotools"> | ||
| <xrefs> | ||
| <xref type="bio.tools">mg-toolkit</xref> | ||
| </xrefs> | ||
| </xml> | ||
| <xml name="creators"> | ||
| <creator> | ||
| <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" /> | ||
| </creator> | ||
| </xml> | ||
| <xml name="citations"> | ||
| <citations> | ||
| <citation type="bibtex"> | ||
| @misc{emg_toolkit, | ||
| author = {EBI Metagenomics}, | ||
| title = {EMG Toolkit}, | ||
| year = {2024}, | ||
| howpublished = {\url{https://github.com/EBI-metagenomics/emg-toolkit}}, | ||
| note = {Accessed: 2024-07-11} | ||
| } | ||
| </citation> | ||
| </citations> | ||
| </xml> | ||
| </macros> |
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| <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> |