Mercurial > repos > ecology > annotations_template

annotate annotations_template.xml @ 2:3e495518e320 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 15:52:46 +0000
parents b99426809978
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b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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1 <tool id="annotations_template" name="Make annotations template" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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2 <description>from scratch or from EML metadata file</description>
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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3 <requirements>
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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4 <requirement type="package" version="4.4.1">r-base</requirement>
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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5 <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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6 </requirements>
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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7 <command detect_errors="exit_code"><![CDATA[
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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8
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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9 #if str($input_prod.input_prod_selector) == "fr_EML"
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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10 mkdir data_files &&
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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11 ln -s $input_prod.inputEML 'data_files/${input_prod.inputEML.element_identifier}';
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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12 #set $eml = $input_prod.inputEML.element_identifier;
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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13 #end if
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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14
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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15 #if str($input_prod.input_prod_selector) == "fr_scratch"
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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16 #set $datatable = ""
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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17 #set $dataother = ""
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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18 #set $datatemp = ""
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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19 mkdir data_files &&
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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20
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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21 #if str($input_prod.input_selector) == "data_table"
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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22 #for $input in $input_prod.input.inputdata
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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23 ln -s $input 'data_files/${input.element_identifier}';
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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24 #set $datatable += $input.element_identifier + " ";
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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25 #end for
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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26 #for $input3 in $input_prod.input.input_temp
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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27 ln -s $input3 'data_files/${input3.element_identifier}';
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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28 #set $datatemp += $input3.element_identifier + " ";
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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29 #end for
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30 #end if
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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31 #if str($input_prod.input_selector) == "other_entities"
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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32
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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33 #for $input2 in $input_prod.input.input_other
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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34 ln -s $input2 'data_files/${input2.element_identifier}';
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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35 #set $dataother += $input2.element_identifier + " ";
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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36 #end for
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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37
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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38 #for $input3 in $input_prod.input.input_temp
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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39 ln -s $input3 'data_files/${input3.element_identifier}';
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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40 #set $datatemp += $input3.element_identifier + " ";
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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41 #end for
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42 #end if
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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43 #if str($input_prod.input_selector) == "both"
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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44
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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45 #for $input in $input_prod.input.inputdata
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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46 ln -s $input 'data_files/${input.element_identifier}';
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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47 #set $datatable += $input.element_identifier + " ";
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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48 #end for
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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49
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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50 #for $input2 in $input_prod.input.input_other
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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51 ln -s $input2 'data_files/${input2.element_identifier}';
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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52 #set $dataother += $input2.element_identifier + " ";
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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53 #end for
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54
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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55 #for $input3 in $input_prod.input.input_temp
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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56 ln -s $input3 'data_files/${input3.element_identifier}';
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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57 #set $datatemp += $input3.element_identifier + " ";
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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58 #end for
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59 #end if
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60 #end if
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61
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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62 Rscript
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63 '$__tool_directory__/annotations_template.R'
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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64 '$input_prod.input_prod_selector'
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65
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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66 #if str($input_prod.input_prod_selector) == "fr_scratch"
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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67 '$input_prod.input.input_selector'
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68
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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69 #if str($input_prod.input.input_selector) =="data_table"
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70 '$datatable'
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71 '$datatemp'
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72 #elif str($input_prod.input.input_selector) =="other_entities"
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73 '$dataother'
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74 '$datatemp'
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75 #elif str($input_prod.input.input_selector) =="both"
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76 '$datatable'
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77 '$dataother'
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78 '$datatemp'
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79 #end if
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80 #elif str($input_prod.input_prod_selector) == "fr_EML"
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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81 '$eml'
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82 #end if
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83
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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84 ]]></command>
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85 <inputs>
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86 <conditional name="input_prod">
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87 <param name="input_prod_selector" type="select" label="How do you want to produce your annotations template ?">
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88 <option value="fr_scratch" selected="true">Make annotations template from scratch</option>
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89 <option value="fr_EML">Make annotations template from an EML file</option>
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90 </param>
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91 <when value="fr_scratch">
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92 <conditional name="input">
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93 <param name="input_selector" type="select" label="What is the type of your data files ?">
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94 <option value="data_table">Data table</option>
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95 <option value="other_entities">Other entities</option>
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96 <option value="both" selected="true">Both data table and other entities</option>
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97 </param>
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98 <when value="data_table">
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99 <param name="inputdata" type="data" format="data" label="Upload all your data tables" multiple= "true"/>
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100 <param name="input_temp" type="data" format="data" label="Upload all metadata template files" multiple= "true" help="This tool needs to be used only after all the metadata templates tools because it needs the other metadata templates to work"/>
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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101 </when>
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102 <when value="other_entities">
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103 <param name="input_other" type="data" format="data" label="Upload all your other entities files" multiple= "true"/>
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104 <param name="input_temp" type="data" format="data" label="Upload all your metadata template files" multiple= "true" help="This tool needs to be used only after all the metadata templates tools because it needs the other metadata templates to work"/>
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105 </when>
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106 <when value="both">
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107 <param name="inputdata" type="data" format="data" label="Upload all your data tables" multiple= "true"/>
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108 <param name="input_other" type="data" format="data" label="Upload all your other entities files" multiple= "true"/>
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109 <param name="input_temp" type="data" format="data" label="Upload all your metadata template files" multiple= "true" help="This tool needs to be used only after all the metadata templates tools because it needs the other metadata templates to work"/>
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110 </when>
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111 </conditional>
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112 </when>
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113 <when value="fr_EML">
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114 <param name="inputEML" type="data" format="xml" label="Upload an EML file" />
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115 </when>
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116 </conditional>
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117 </inputs>
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118 <outputs>
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119 <data name="output" from_work_dir="data_files/annotations.txt" format="txt" label="annotations.txt"/>
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120 </outputs>
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121 <tests>
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122 <test expect_num_outputs="1">
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123 <param name="input_prod_selector" value="fr_EML"/>
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124 <param name="inputEML" value="Assessing_the_importance_of_field_margins_for_bat_species.xml"/>
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125 <output name="output" file="annotemp/annotations_template.txt"/>
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126 </test>
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127 <test expect_num_outputs="1">
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128 <param name="input_prod_selector" value="fr_scratch"/>
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129 <param name="input_selector" value="both"/>
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130 <param name="inputdata" value = "annotemp/ceamarc_env.tsv"/>
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131 <param name="input_other" value="annotemp/pivot_wider_jupytool_notebook.ipynb"/>
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132 <param name="input_temp" value="annotemp/abstract.txt,annotemp/personnel.txt,annotemp/keywords.txt,annotemp/geographic_coverage.txt,annotemp/methods.txt,annotemp/custom_units.txt,annotemp/attributes_ceamarc_env.txt"/>
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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133 <output name="output" file="annotemp/annotations_template_2.txt"/>
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134 </test>
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135 <test expect_num_outputs="1">
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136 <param name="input_prod_selector" value="fr_scratch"/>
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137 <param name="input_selector" value="data_table"/>
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138 <param name="inputdata" value = "annotemp/ceamarc_env.tsv"/>
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139 <param name="input_temp" value="annotemp/abstract.txt,annotemp/personnel.txt,annotemp/keywords.txt,annotemp/geographic_coverage.txt,annotemp/methods.txt,annotemp/custom_units.txt,annotemp/attributes_ceamarc_env.txt"/>
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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140 <output name="output" file="annotemp/annotations_template_3.txt"/>
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141 </test>
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142 <test expect_num_outputs="1">
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143 <param name="input_prod_selector" value="fr_scratch"/>
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144 <param name="input_selector" value="other_entities"/>
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145 <param name="input_other" value="annotemp/pivot_wider_jupytool_notebook.ipynb"/>
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146 <param name="input_temp" value="annotemp/abstract.txt,annotemp/personnel.txt,annotemp/keywords.txt,annotemp/geographic_coverage.txt,annotemp/methods.txt,annotemp/custom_units.txt,annotemp/attributes_ceamarc_env.txt"/>
b99426809978 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
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147 <output name="output" file="annotemp/annotations_template_4.txt"/>
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148 </test>
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149 </tests>
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150 <help><![CDATA[
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151
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152 **What it does?**
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153 --------------------
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154
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155 This tool is made to produce an annotation template to adds semantic meaning to dataset features (variables, locations, persons, etc.) through links to ontology terms. Template produced can be used in the make EML tool to produce EML metadata Annotating a dataset enables greater human understanding and machine actionability (linked data) and vastly improves the accuracy of future user searches and the interoperability of data in general.
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156
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157 **How to use it?**
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158 --------------------
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159
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160 You can run this tool after all your EAL metadata templates are complete or if you're annotating an existing EML file.
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161
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162 If you use an existing EML file you will need to input it.
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163 If you want to generate annotation template from scratch you will need to input your data files and all the other complete template that you produce before with the other EMLassemblyline tools.
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164
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165 .. class:: infomark
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166
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167 If you use an existing EML file to generate annotation template you can use **eml2eal** tool to produce annotation template and all the other templates.
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168
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169 ]]></help>
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170 <citations>
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171 <citation type="bibtex">@Manual{,
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172 title = {EMLassemblyline: A tool kit for building EML metadata workflows},
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173 author = {Colin Smith},
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174 year = {2022},
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175 note = {https://github.com/EDIorg/EMLassemblyline,
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176 https://ediorg.github.io/EMLassemblyline/},
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177 }</citation>
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178 </citations>
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179 </tool>