Workflow Type:  Galaxy
        
  
        
          
            
              
    
      
        
        
    
    
      
        
        
    
    
      
        
        
    
            
          
        
        
      
  
    
      
        
      
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            Work-in-progress
        
        
Workflow to take DataOne data packages (raw datasets + metadata written in Ecological Metadata Standard) as input and create a DwC occurence.csv file almost ready to put in a Dawrin core Archive using eml-annotations at the attribute level
Inputs
| ID | Name | Description | Type | 
|---|---|---|---|
| BDD_Kakila_v2_2021021_observateur.tsv | BDD_Kakila_v2_2021021_observateur.tsv | n/a | 
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| BDD_Kakila_v2_20210221_observation.tsv | BDD_Kakila_v2_20210221_observation.tsv | n/a | 
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| BDD_Kakila_v2_20210221_organisme.tsv | BDD_Kakila_v2_20210221_organisme.tsv | n/a | 
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| BDD_Kakila_v2_20210221_secteur_geog.tsv | BDD_Kakila_v2_20210221_secteur_geog.tsv | n/a | 
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| BDD_Kakila_v2_20210221_sortie.tsv | BDD_Kakila_v2_20210221_sortie.tsv | n/a | 
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| BDD_Kakila_v2_20210221_taxon.tsv | BDD_Kakila_v2_20210221_taxon.tsv | n/a | 
 | 
| Kakila_database_of_marine_mammal_observation_data_in_the_AGOA_sanctuary_-_French_Antilles.xml | Kakila_database_of_marine_mammal_observation_data_in_the_AGOA_sanctuary_-_French_Antilles.xml | n/a | 
 | 
Steps
| ID | Name | Description | 
|---|---|---|
| 7 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 | 
| 8 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 | 
| 9 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 | 
| 10 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 | 
| 11 | Select | Grep1 | 
| 12 | Select | Grep1 | 
| 13 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 | 
| 14 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 | 
| 15 | Regex Replace | toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0 | 
| 16 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 | 
| 17 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 | 
| 18 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 | 
| 19 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 | 
| 20 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 | 
| 21 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 | 
| 22 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0 | 
| 23 | Filter Tabular | toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0 | 
| 24 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 | 
| 25 | Unique | toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3 | 
| 26 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0 | 
| 27 | Remove beginning | Remove beginning1 | 
Outputs
| ID | Name | Description | Type | 
|---|---|---|---|
| _anonymous_output_1 | _anonymous_output_1 | n/a | 
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| _anonymous_output_2 | _anonymous_output_2 | n/a | 
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| _anonymous_output_3 | _anonymous_output_3 | n/a | 
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| _anonymous_output_4 | _anonymous_output_4 | n/a | 
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| _anonymous_output_5 | _anonymous_output_5 | n/a | 
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| _anonymous_output_6 | _anonymous_output_6 | n/a | 
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| _anonymous_output_7 | _anonymous_output_7 | n/a | 
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| _anonymous_output_8 | _anonymous_output_8 | n/a | 
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| _anonymous_output_9 | _anonymous_output_9 | n/a | 
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| _anonymous_output_10 | _anonymous_output_10 | n/a | 
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| _anonymous_output_11 | _anonymous_output_11 | n/a | 
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| _anonymous_output_12 | _anonymous_output_12 | n/a | 
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| _anonymous_output_13 | _anonymous_output_13 | n/a | 
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| _anonymous_output_14 | _anonymous_output_14 | n/a | 
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| _anonymous_output_15 | _anonymous_output_15 | n/a | 
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| _anonymous_output_16 | _anonymous_output_16 | n/a | 
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| _anonymous_output_17 | _anonymous_output_17 | n/a | 
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| _anonymous_output_18 | _anonymous_output_18 | n/a | 
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| _anonymous_output_19 | _anonymous_output_19 | n/a | 
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| _anonymous_output_20 | _anonymous_output_20 | n/a | 
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| _anonymous_output_21 | _anonymous_output_21 | n/a | 
 | 
Version History
Version 1 (earliest) Created 9th Apr 2021 at 16:45 by Yvan Le Bras
Added/updated 1 files
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master7dbdd02
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Views: 6539 Downloads: 819 Runs: 0
Created: 9th Apr 2021 at 16:45
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 https://orcid.org/0000-0002-8504-068X
 https://orcid.org/0000-0002-8504-068X
