Mercurial > repos > ecology > taxo_cov_template
annotate taxo_cov_template.xml @ 1:0cfc9b6da2ac draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 5c327a780dc58fb954e7b65db6fd413ee3909c84
author | ecology |
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date | Mon, 04 Dec 2023 21:48:41 +0000 |
parents | 4cd3d9fdb5f3 |
children | 2af7401f13e0 |
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4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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1 <tool id="taxo_cov_template" name="Make taxonomic coverage template" version="0.1.0+galaxy0" profile="22.05"> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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2 <description>for EML metadata creation</description> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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3 <requirements> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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4 <requirement type="package" version="4.3.1">r-base</requirement> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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5 <requirement type="package" version="3.5.5">r-emlassemblyline</requirement> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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6 </requirements> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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7 <command detect_errors="exit_code"><![CDATA[ |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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8 |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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9 mkdir data_files && |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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10 ln -s '$inputdata' 'data_files/${inputdata.element_identifier}'; |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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11 #set $table = $inputdata.element_identifier; |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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12 |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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13 Rscript |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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14 '$__tool_directory__/taxo_cov_template.R' |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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15 '$inputdata' |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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16 '$table' |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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17 '$taxa_col' |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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18 '$name_type' |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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19 '$authority.authority_name' |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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20 '$authority.authority_name2' |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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21 '$authority.authority_name3' |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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22 '$empty' |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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23 |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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24 ]]></command> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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25 <inputs> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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26 <param name="inputdata" type="data" format="tabular" label="Upload table containing all unique taxa in the data" /> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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27 <param name="taxa_col" type="data_column" label="What column of your table listing all unique taxa ?" data_ref="inputdata" /> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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28 <param name="name_type" type="select" label="What type of taxa name are in your table ?"> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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29 <option value="scientific">Scientific</option> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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30 <option value="common">Common</option> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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31 </param> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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32 <section name="authority" title="Select the taxonomic authority in wich the taxa's name will be search (you can select multiple authority). If you select several authhority, please select in order of decreasing in preference." > |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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33 <param name="authority_name" type="select" label="Select your first taxonomic authority in wich the taxa's name will be search. (required)" optional="false"> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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34 <option value="11">GBIF</option> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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35 <option value="9">WORMS</option> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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36 <option value="3">ITIS</option> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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37 </param> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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38 <param name="authority_name2" type="select" label="Select if you want a second taxonomic authority in wich the taxa's name will be search, else select 'None'."> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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39 <option value="0">None</option> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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40 <option value="11">GBIF</option> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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41 <option value="9">WORMS</option> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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42 <option value="3">ITIS</option> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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43 </param> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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44 <param name="authority_name3" type="select" label="Select if you want a third taxonomic authority in wich the taxa's name will be search, else select 'None'."> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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45 <option value="0">None</option> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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46 <option value="11">GBIF</option> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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47 <option value="9">WORMS</option> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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48 <option value="3">ITIS</option> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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49 </param> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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50 </section> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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51 <param name="empty" type="boolean" label="Write an empty template file ?" /> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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52 </inputs> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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53 <outputs> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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54 <data name="output" from_work_dir="taxonomic_coverage.txt" format="txt" label="Taxonomic coverage template"/> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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55 </outputs> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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56 <tests> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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57 <test> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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58 <param name="inputdata" value="taxa.tsv"/> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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59 <param name="taxa_col" value="1"/> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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60 <param name="name_type" value="scientific"/> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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61 <param name="authority_name" value="11"/> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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62 <param name="authority_name2" value="0"/> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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63 <param name="authority_name3" value="0"/> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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64 <param name="empty" value="false"/> |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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65 <output name="output" value="taxonomic_coverage.txt"/> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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66 </test> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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67 </tests> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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68 <help><![CDATA[ |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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69 **What it does?** |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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70 -------------------- |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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71 |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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72 This tool produce template for EML metadata. It produce templates for taxonomic coverage. |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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73 This tool can be used with the "Make templates for core features of a data package" tool before the "make eml" tool. |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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74 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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75 **How to use it?** |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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76 -------------------- |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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77 To use this tool, you need to upload a table with a column containing a list of all unique taxa present in the data (example below), then select wich column of your table contains the taxa's names, select what type of taxa name it is (scientific or common) and select the taxonomic authority in wich the taxa's name will be search (ITIS,WORMS or/and GBIF). If you select several authhority, please select in order in ordered of ID's decreasing in preference. |
4cd3d9fdb5f3
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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78 You can also decide to make an empty taxonomic coverage templates. |
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79 |
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80 |
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81 **Example of taxonomic table :** |
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82 ----------------------------------------- |
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83 |
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84 +-------------------+-------------------+ |
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85 | taxa | site | |
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86 +-------------------+-------------------+ |
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87 | Achelia sp | 1 | |
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88 +-------------------+-------------------+ |
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89 | Achelia spicata | 2 | |
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90 +-------------------+-------------------+ |
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91 | Achelia suflata | 2 | |
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92 +-------------------+-------------------+ |
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93 | Ammothea adunca | 3 | |
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94 +-------------------+-------------------+ |
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95 | ... | ... | |
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96 +-------------------+-------------------+ |
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97 ]]></help> |
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98 </tool> |