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_20210221_taxon.tsv BDD_Kakila_v2_20210221_taxon.tsv n/a n/a
BDD_Kakila_v2_2021021_observateur.tsv BDD_Kakila_v2_2021021_observateur.tsv n/a n/a
BDD_Kakila_v2_20210221_observation.tsv BDD_Kakila_v2_20210221_observation.tsv n/a n/a
BDD_Kakila_v2_20210221_organisme.tsv BDD_Kakila_v2_20210221_organisme.tsv n/a n/a
BDD_Kakila_v2_20210221_secteur_geog.tsv BDD_Kakila_v2_20210221_secteur_geog.tsv n/a n/a
BDD_Kakila_v2_20210221_sortie.tsv BDD_Kakila_v2_20210221_sortie.tsv n/a 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 n/a

Steps

ID Name Description
0 BDD_Kakila_v2_20210221_taxon.tsv
1 BDD_Kakila_v2_2021021_observateur.tsv
2 BDD_Kakila_v2_20210221_observation.tsv
3 BDD_Kakila_v2_20210221_organisme.tsv
4 BDD_Kakila_v2_20210221_secteur_geog.tsv
5 BDD_Kakila_v2_20210221_sortie.tsv
6 Kakila_database_of_marine_mammal_observation_data_in_the_AGOA_sanctuary_-_French_Antilles.xml
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
output output n/a input
output output n/a input
output output n/a input
output output n/a input
out_file1 out_file1 n/a input
out_file1 out_file1 n/a input
output output n/a input
output output n/a input
outfile outfile n/a txt
output output n/a input
output output n/a input
out_file1 out_file1 n/a input
output output n/a input
output output n/a input
out_file1 out_file1 n/a input
out_file out_file n/a tabular
output output n/a tabular
output output n/a input
outfile outfile n/a input
out_file out_file n/a tabular
out_file1 out_file1 n/a input
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Views: 389   Downloads: 21

Created: 9th Apr 2021 at 16:45

Last used: 6th Dec 2021 at 19:58

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

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