Workflow constructed from history 'test dwc from PNDB Data package EML DwC annotations'
Version 1

Workflow Type: Galaxy
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
  • File
BDD_Kakila_v2_20210221_observation.tsv BDD_Kakila_v2_20210221_observation.tsv n/a
  • File
BDD_Kakila_v2_20210221_organisme.tsv BDD_Kakila_v2_20210221_organisme.tsv n/a
  • File
BDD_Kakila_v2_20210221_secteur_geog.tsv BDD_Kakila_v2_20210221_secteur_geog.tsv n/a
  • File
BDD_Kakila_v2_20210221_sortie.tsv BDD_Kakila_v2_20210221_sortie.tsv n/a
  • File
BDD_Kakila_v2_20210221_taxon.tsv BDD_Kakila_v2_20210221_taxon.tsv n/a
  • File
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
  • File

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
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Version History

Version 1 (earliest) Created 9th Apr 2021 at 16:45 by Yvan Le Bras

Added/updated 1 files


Open master 7dbdd02
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Views: 3654   Downloads: 277   Runs: 0

Created: 9th Apr 2021 at 16:45

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Total size: 48.8 KB
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