Mercurial > repos > ecology > geo_cov_template

annotate geo_cov_template.xml @ 2:b14e398fee7f 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 15:51:30 +0000
parents e1b8dad192ee
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e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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1 <tool id="geo_cov_template" name="Make geographic coverage template" version="0.1.0+galaxy0" profile="22.05">
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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2 <description>for EML metadata creation</description>
e1b8dad192ee 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>
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5 </requirements>
e1b8dad192ee 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
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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8 mkdir data_files &&
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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9 ln -s '$inputdata' 'data_files/${inputdata.element_identifier}' &&
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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10 #set $table = $inputdata.element_identifier
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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11
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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12 Rscript
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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13 '$__tool_directory__/geo_cov_temp.R'
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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14 '$inputdata'
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15 '$table'
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16 '$lat_col'
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17 '$long_col'
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18 '$site_col'
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19 '$empty'
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20
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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21 ]]></command>
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22 <inputs>
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23 <param name="inputdata" type="data" format="tabular" label="Upload table containing geographic coordinates" />
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24 <param name="lat_col" type="data_column" label="What column of your table contains latitude coordinates in decimal degrees?" data_ref="inputdata" use_header_names="true"/>
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25 <param name="long_col" type="data_column" label="What column of your table contains longitude coordinates in decimal degrees ?" data_ref="inputdata" use_header_names="true"/>
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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26 <param name="site_col" type="data_column" label="What column of your table contains site names ?" data_ref="inputdata" use_header_names="true"/>
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27 <param name="empty" type="boolean" label="Write an empty template file ?" />
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28 </inputs>
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29 <outputs>
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30 <data name="output" from_work_dir="geographic_coverage.txt" format="txt" label="geographic_coverage.txt"/>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="inputdata" value="test_geocov.tsv"/>
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35 <param name="lat_col" value="2"/>
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36 <param name="long_col" value="3"/>
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37 <param name="site_col" value="1"/>
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38 <param name="empty" value="false"/>
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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39 <output name="output" value="geographic_coverage.txt"/>
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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44 **What it does?**
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45 --------------------
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46
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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47 This tool produce template for EML metadata. It produce template for geographic coverage.
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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48 After that, these files can be edited to add information about your data and then be used in the make eml tool to produce EML metadata.
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49
e1b8dad192ee planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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50 **How to use it?**
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51 --------------------
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52 To use this tool, you need to upload a table containing geographic coordinates (the decimal separator must be ".", example below), then select wich column of your table contains latitude, longitude and site names. You can also decide to make an empty geografical coverage templates.
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53
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54
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55 **Example of geographic table :**
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56 -----------------------------------------
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57
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58 +------+------+----------------------+
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59 | long | lat | site |
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60 +------+------+----------------------+
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61 |139.22|-65.57| name of site 1 |
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62 +------+------+----------------------+
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63 |139.22|-65.57| name of site 2 |
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64 +------+------+----------------------+
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65 | ... | ... | ... |
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66 +------+------+----------------------+
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67 ]]></help>
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68 <citations>
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69 <citation type="bibtex">@Manual{,
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70 title = {EMLassemblyline: A tool kit for building EML metadata workflows},
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71 author = {Colin Smith},
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72 year = {2022},
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73 note = {https://github.com/EDIorg/EMLassemblyline,
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74 https://ediorg.github.io/EMLassemblyline/},
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75 }</citation>
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76 </citations>
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77 </tool>