Mercurial > repos > iuc > mg_toolkit

annotate original_metadata.xml @ 0:ae351724edfc draft default tip

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