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author ecology
date Thu, 16 Jan 2025 15:54:31 +0000
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1 <tool id="eal_table_template" name="Make templates for data tables" version="0.1.1+galaxy0" profile="22.05">
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2 <description>attributes and categorical variables for EML metadata creation</description>
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3 <requirements>
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4 <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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8 #set $table = ""
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9 mkdir data_files &&
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10 #for $indata in $inputdata
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11 ln -s '$indata' 'data_files/${indata.element_identifier}' &&
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12 #set $table += $indata.element_identifier + " "
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13 #end for
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15 Rscript
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16 '$__tool_directory__/eal_table_templates.R'
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17 '$table'
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19 ]]></command>
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20 <inputs>
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21 <param name="inputdata" type="data_collection" collection_type="list" label="Upload all data files wich are data table" help= "Input a data collection."/>
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22 </inputs>
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23 <outputs>
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24 <collection name="templates" type="list" label="Data table templates">
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25 <discover_datasets pattern="(?P&lt;designation&gt;.+\.txt)" format="txt"/>
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26 </collection>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="inputdata">
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31 <collection type="list">
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32 <element name="datafile_1.tsv" value="datafile_1.tsv" />
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33 </collection>
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34 </param>
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35 <output_collection name='templates' type = "list" count="2"/>
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 **What it does?**
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40 --------------------
6de4b4f70b7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32
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41 This tool is used to produce EAL templates for data table used to build EML metadata. It produces the following eal files:
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42
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43 - attibutes_my_datatable.txt (describe the attributes of your data table)
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44 - catvars_mydatatable.txt (only if there are one or more catégorical variable in your data table)
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45 - custom_units.txt (made to describe custom units if there are any)
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47 After that, these files can be edited to add information about your data table and then be used in the make eml tool to produce EML metadata.
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49 **How to use it?**
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50 --------------------
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52 To use this tool, you need to select, in your history a data collection with your data table (one or more). To do so, you can select the **Upload file** tool, select the *Collection* tab, upload all your data table file, click on the *Start* button to integrate the files to Galaxy and then click on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates. You also can upload your files to Galaxy, select them in the history by clicking the *Select items* button, click on the newly appeared box on the right and select *Build dataset list*.
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53
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54 ]]></help>
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55 <citations>
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56 <citation type="bibtex">@Manual{,
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57 title = {EMLassemblyline: A tool kit for building EML metadata workflows},
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58 author = {Colin Smith},
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59 year = {2022},
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60 note = {https://github.com/EDIorg/EMLassemblyline,
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61 https://ediorg.github.io/EMLassemblyline/},
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62 }</citation>
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63 </citations>
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64 </tool>