mapseq-to-ampvis2/main
v0.1

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Workflow Type: Galaxy

The MAPseq to Ampvis workflow processes MAPseq OTU tables and associated metadata for analysis in Ampvis2. This workflow involves reformatting MAPseq output datasets to produce structured output files suitable for Ampvis2.

SEEK ID: https://workflowhub.eu/workflows/1275?version=1

Inputs

ID Name Description Type
MAPseq OTU tables #main/MAPseq OTU tables A dataset collection containing the tab-separated OTU outputs of MAPseq.
  • array containing
    • File
OTU table metadata #main/OTU table metadata Contextual information associated with the data from the OTU tables.
  • File

Steps

ID Name Description
2 Query Tabular toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
3 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
4 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
5 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
6 Column join toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3
7 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
8 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
9 Query Tabular toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
10 ampvis2 load toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.9+galaxy0

Outputs

ID Name Description Type
Ampvis2 metadata table #main/Ampvis2 metadata table n/a
  • File
Ampvis2 object #main/Ampvis2 object n/a
  • File
Ampvis2 taxonomy table #main/Ampvis2 taxonomy table n/a
  • File
OTU table #main/OTU table n/a
  • File
Taxonomy table #main/Taxonomy table n/a
  • File

Version History

v0.1 (earliest) Created 4th Feb 2025 at 03:02 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 5c51897
help Creators and Submitter
Creators
  • Rand Zoabi
  • Mara Besemer
Submitter
Tool
ampvis
License
MIT License
Activity

Views: 6   Downloads: 2   Runs: 0

Created: 4th Feb 2025 at 03:02

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