Population and community metrics calculation from Biodiversity data Version 2
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Run on usegalaxy.euGalaxy-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: 467 Downloads: 30
Created: 24th Jul 2020 at 13:27
Last updated: 24th Jul 2020 at 14:00
Last used: 10th May 2021 at 21:23
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Version History
Version 2 (latest) Created 24th Jul 2020 at 14:00 by Yvan Le Bras
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Teams: PNDB
Organizations: French Museum of Natural History, ff
https://orcid.org/0000-0003-4308-5617
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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, Ay Lab, iPC: individualizedPaediatricCure
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French Biodiversity e-infrastructure
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