Mercurial > repos > ecology > vector_template
comparison vector_template.xml @ 0:330f15f2ad3f draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32
| author | ecology |
|---|---|
| date | Sat, 23 Dec 2023 20:40:29 +0000 |
| parents | |
| children | c65dd54f9807 |
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| -1:000000000000 | 0:330f15f2ad3f |
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| 1 <tool id="vector_template" name="Make templates for vector files" version="0.1.0+galaxy0" profile="22.05"> | |
| 2 <description>attributes for EML metadata creation</description> | |
| 3 <requirements> | |
| 4 <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 | |
| 8 #set $table = "" | |
| 9 mkdir data_files && | |
| 10 | |
| 11 #for $indata in $inputdata | |
| 12 ln -s '$indata' 'data_files/${indata.element_identifier}'; | |
| 13 #set $table += $indata.element_identifier + " "; | |
| 14 #end for | |
| 15 | |
| 16 Rscript | |
| 17 '$__tool_directory__/vector_templates.R' | |
| 18 '$table' | |
| 19 | |
| 20 | |
| 21 ]]></command> | |
| 22 <inputs> | |
| 23 <param name="inputdata" type="data_collection" collection_type="list" label="Upload all data files wich are vector files" help= "Input a data collection."/> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <collection name="templates" type="list" label="Templates for vector data"> | |
| 27 <discover_datasets pattern="(?P<designation>.+\.txt)" format="txt"/> | |
| 28 </collection> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="inputdata"> | |
| 33 <collection type="list"> | |
| 34 <element name="data_7.GeoJSON" value="data_7.GeoJSON"/> | |
| 35 </collection> | |
| 36 </param> | |
| 37 <output_collection name='templates' type = "list" count="3"/> | |
| 38 </test> | |
| 39 </tests> | |
| 40 <help><![CDATA[ | |
| 41 | |
| 42 **What it does?** | |
| 43 -------------------- | |
| 44 | |
| 45 This tool is used to produce EAL templates for data table used to build EML metadata. It produces the following eal files: | |
| 46 | |
| 47 - attibutes_my_vector.txt (describe the attributes of your vector file) | |
| 48 - catvars_my_vector.txt (only if there are one or more catégorical variable in your vector file) | |
| 49 - custom_units.txt (made to describe custom units if there are any) | |
| 50 | |
| 51 After that, these files can be edited to add information about your vector file and then be used in the make eml tool to produce EML metadata. | |
| 52 | |
| 53 **How to use it?** | |
| 54 -------------------- | |
| 55 To use this tool, you need to select, in your history a data collection with your vector data file(s) (format GeoJSON). To do so, you can select the **Upload file** tool, select the *Collection* tab, upload all your templates, 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*. To upload shapefile you need to create a composite data. | |
| 56 | |
| 57 .. class:: warningmark | |
| 58 '''TIP''' This tool dont accept as inputs composite data like shapefile at the moment. | |
| 59 | |
| 60 ]]></help> | |
| 61 </tool> |