Mercurial > repos > iuc > mg_toolkit
comparison original_metadata.xml @ 0:ae351724edfc draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg-toolkit commit b21f516390fcbbe3c098266ff0d72e64924aab00
| author | iuc |
|---|---|
| date | Fri, 12 Jul 2024 15:09:56 +0000 |
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| -1:000000000000 | 0:ae351724edfc |
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| 1 <tool id="mg_toolkit_original_metadata" name="Metagenomics toolkit Original Metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> | |
| 2 <description>Download original metadata for a study</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="creators" /> | |
| 7 <expand macro="biotools" /> | |
| 8 <expand macro="requirements" /> | |
| 9 <command><![CDATA[ | |
| 10 mkdir output_metadata && | |
| 11 mg-toolkit original_metadata -a ${accessions} && | |
| 12 mv *.csv output_metadata | |
| 13 ]]></command> | |
| 14 | |
| 15 <inputs> | |
| 16 <param name="accessions" type="text" label="Accessions" help="Study/project accessions (e.g., ERP001736 SRP000319)" optional="false"> | |
| 17 <validator type="regex" message="Accessions separated with white spaces">^([A-Za-z]{3,4}\d+)(\s[A-Za-z]{3,4}\d+)*$</validator> | |
| 18 </param> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <collection name="output_collection" type="list" label="Original metadata"> | |
| 22 <discover_datasets pattern="(?P<designation>.+).csv" directory="output_metadata" format="csv"/> | |
| 23 </collection> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test> | |
| 27 <param name="accessions" value="ERP001736 SRP000319" /> | |
| 28 <output_collection name="output_collection" type="list"> | |
| 29 <element name="ERP001736"> | |
| 30 <assert_contents> | |
| 31 <has_n_lines n="250" /> | |
| 32 <has_size size="185577" /> | |
| 33 </assert_contents> | |
| 34 </element> | |
| 35 <element name="SRP000319"> | |
| 36 <assert_contents> | |
| 37 <has_n_lines n="30" /> | |
| 38 <has_size size="2855" /> | |
| 39 </assert_contents> | |
| 40 </element> | |
| 41 </output_collection> | |
| 42 </test> | |
| 43 <test> | |
| 44 <param name="accessions" value="ERP001736" /> | |
| 45 <output_collection name="output_collection" type="list"> | |
| 46 <element name="ERP001736"> | |
| 47 <assert_contents> | |
| 48 <has_n_lines n="250" /> | |
| 49 <has_size size="185577" /> | |
| 50 </assert_contents> | |
| 51 </element> | |
| 52 </output_collection> | |
| 53 </test> | |
| 54 </tests> | |
| 55 <help> | |
| 56 <![CDATA[ | |
| 57 The mg-toolkit original-metadata tool is part of the EMG Toolkit provided by EBI Metagenomics. | |
| 58 This tool allows users to retrieve the original metadata associated with metagenomic studies and analyses. | |
| 59 It facilitates the extraction of detailed contextual information submitted by researchers, | |
| 60 aiding in the interpretation and further analysis of metagenomic data. | |
| 61 | |
| 62 License | |
| 63 ------- | |
| 64 * `Apache-2.0 license <https://raw.githubusercontent.com/EBI-Metagenomics/emg-toolkit/master/LICENSE>`_ | |
| 65 | |
| 66 ]]> | |
| 67 </help> | |
| 68 <expand macro="citations" /> | |
| 69 </tool> |