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annotate vector_template.xml @ 2:4483d483499b draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 61182ba790bdeeb98750403b869051ccad1a736c
author ecology
date Thu, 16 Jan 2025 15:53:28 +0000
parents f8dad04c9efa
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f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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1 <tool id="vector_template" name="Make templates for vector files" version="0.1.0+galaxy0" profile="22.05">
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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2 <description>attributes for EML metadata creation</description>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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3 <requirements>
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4 <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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5 </requirements>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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6 <command detect_errors="exit_code"><![CDATA[
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7
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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8 #set $table = ""
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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9 mkdir data_files &&
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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11 #for $indata in $inputdata
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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12 ln -s '$indata' 'data_files/${indata.element_identifier}';
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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13 #set $table += $indata.element_identifier + " ";
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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14 #end for
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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16 Rscript
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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17 '$__tool_directory__/vector_templates.R'
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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18 '$table'
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f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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21 ]]></command>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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22 <inputs>
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23 <param name="inputdata" type="data_collection" collection_type="list" label="Upload all data files wich are vector files" help= "Input a data collection."/>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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24 </inputs>
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25 <outputs>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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26 <collection name="templates" type="list" label="Templates for vector data">
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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27 <discover_datasets pattern="(?P&lt;designation&gt;.+\.txt)" format="txt"/>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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28 </collection>
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29 </outputs>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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30 <tests>
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31 <test>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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32 <param name="inputdata">
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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33 <collection type="list">
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34 <element name="data_7.GeoJSON" value="data_7.GeoJSON"/>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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35 </collection>
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36 </param>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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37 <output_collection name='templates' type = "list" count="3"/>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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38 </test>
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39 </tests>
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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40 <help><![CDATA[
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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42 **What it does?**
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43 --------------------
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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45 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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46
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47 - attibutes_my_vector.txt (describe the attributes of your vector file)
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48 - catvars_my_vector.txt (only if there are one or more catégorical variable in your vector file)
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49 - custom_units.txt (made to describe custom units if there are any)
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50
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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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.
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52
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53 **How to use it?**
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54 --------------------
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f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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56 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.
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57
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58 .. class:: warningmark
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59
f8dad04c9efa planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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60 '''TIP''' This tool dont accept as inputs composite data like shapefile at the moment.
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61
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62 ]]></help>
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63 <citations>
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64 <citation type="bibtex">@Manual{,
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65 title = {EMLassemblyline: A tool kit for building EML metadata workflows},
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66 author = {Colin Smith},
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67 year = {2022},
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68 note = {https://github.com/EDIorg/EMLassemblyline,
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69 https://ediorg.github.io/EMLassemblyline/},
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70 }</citation>
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71 </citations>
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72 </tool>