Population and community metrics calculation from Biodiversity data Version 2
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Galaxy-E (ecology.usegalaxy.eu) workflow to calculate species presence / absence, community metrics and compute generalized linear models to identify effects and significativity of these effects on biodiversity.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| input | input | runtime parameter for tool Calculate community metrics | n/a |
Steps
| ID | Name | Description |
|---|---|---|
| 0 | Observations | Species count. A tabular file with observation data. Must at least contain three columns 'observation.unit' which associate year and location (alternatively, you can have this column splited in 2 columns named 'year' and 'location'), 'species.code' with species ID and 'number' for abundance. |
| 1 | Unitobs | Sampling sites geographical and temporal informations |
| 2 | Calculate community metrics | toolshed.g2.bx.psu.edu/repos/ecology/pampa_communitymetrics/pampa_communitymetrics/0.0.1 |
| 3 | Calculate presence absence table | toolshed.g2.bx.psu.edu/repos/ecology/pampa_presabs/pampa_presabs/0.0.1 |
| 4 | Compute GLM on community data | toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmcomm/pampa_glmcomm/0.0.1 |
| 5 | Compute GLM on population data | toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmsp/pampa_glmsp/0.0.1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| output_community | output_community | n/a | tabular |
| output_presabs | output_presabs | n/a | tabular |
| output_summary | output_summary | n/a | tabular |
| output_recap | output_recap | n/a | txt |
| output_rate | output_rate | n/a | txt |
| output_summary | output_summary | n/a | tabular |
| output_recap | output_recap | n/a | txt |
| output_rate | output_rate | n/a | txt |
Creators and Submitter
Views: 384 Downloads: 25
Created: 24th Jul 2020 at 13:27
Last updated: 24th Jul 2020 at 14:00
Last used: 1st Mar 2021 at 09:10
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Version History
Version 2 (latest) Created 24th Jul 2020 at 14:00 by Yvan Le Bras
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https://orcid.org/0000-0002-8504-068X
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, Australian BioCommons, virAnnot pipeline
Web page: Not specified
French Biodiversity e-infrastructure
Space: Independent Teams
Public web page: https://www.pndb.fr/
