Compute and analyze biodiversity metrics with PAMPA toolsuite 1.0
Visit source
Download RO-Crate
Run on GalaxyCompute and analyze biodiversity metrics with PAMPA toolsuite
Associated Tutorial
This workflows is part of the tutorial Compute and analyze biodiversity metrics with PAMPA toolsuite, available in the GTN
Thanks to...
Tutorial Author(s): Coline Royaux, Yvan Le Bras, Dominique Pelletier, Jean-Baptiste Mihoub
Tutorial Contributor(s): Helena Rasche, Yvan Le Bras, Saskia Hiltemann, Coline Royaux, Björn Grüning
Funder(s): Pôle National de Données de Biodiversité
Grants(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 |
| 4 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 |
| 5 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0 |
| 6 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 |
| 7 | Merge Columns | toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2 |
| 8 | Merge Columns | toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2 |
| 9 | Count | Count1 |
| 10 | Filter | Filter1 |
| 11 | Merge Columns | toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2 |
| 12 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0 |
| 13 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0 |
| 14 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 |
| 15 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0 |
| 16 | Calculate presence absence table | toolshed.g2.bx.psu.edu/repos/ecology/pampa_presabs/pampa_presabs/0.0.2 |
| 17 | Calculate presence absence table | toolshed.g2.bx.psu.edu/repos/ecology/pampa_presabs/pampa_presabs/0.0.2 |
| 18 | Merge Columns | toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2 |
| 19 | Calculate presence absence table | toolshed.g2.bx.psu.edu/repos/ecology/pampa_presabs/pampa_presabs/0.0.2 |
| 20 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0 |
| 21 | Calculate community metrics | toolshed.g2.bx.psu.edu/repos/ecology/pampa_communitymetrics/pampa_communitymetrics/0.0.2 |
| 22 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0 |
| 23 | Merge Columns | toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2 |
| 24 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 |
| 25 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 |
| 26 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 |
| 27 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0 |
| 28 | Compute GLM on community data | toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmcomm/pampa_glmcomm/0.0.2 |
| 29 | Compute GLM on population data | toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmsp/pampa_glmsp/0.0.2 |
| 30 | Compute GLM on population data | toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmsp/pampa_glmsp/0.0.2 |
| 31 | Compute GLM on population data | toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmsp/pampa_glmsp/0.0.2 |
| 32 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0 |
| 33 | Create a plot from GLM data | toolshed.g2.bx.psu.edu/repos/ecology/pampa_plotglm/pampa_plotglm/0.0.2 |
| 34 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0 |
| 35 | Create a plot from GLM data | toolshed.g2.bx.psu.edu/repos/ecology/pampa_plotglm/pampa_plotglm/0.0.2 |
| 36 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0 |
| 37 | Create a plot from GLM data | toolshed.g2.bx.psu.edu/repos/ecology/pampa_plotglm/pampa_plotglm/0.0.2 |
| 38 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0 |
| 39 | Create a plot from GLM data | toolshed.g2.bx.psu.edu/repos/ecology/pampa_plotglm/pampa_plotglm/0.0.2 |
Version History
master
Creators and Submitter
Views: 47 Downloads: 6 Runs: 0
Created: 2nd Jun 2025 at 11:04
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
