[Microbiome] New tutorial: Annotate MGEs in metagenomics data using custom database #5646
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bgruening
reviewed
Dec 17, 2024
| @@ -758,7 +761,7 @@ Let's extract an overview of the annotations per metagenomic sequence by groupin | |||
| > | |||
| > 3. {% tool [Add Header](toolshed.g2.bx.psu.edu/repos/estrain/add_column_headers/add_column_headers/0.1.3) %} with the following parameters: | |||
| > - *"List of Column headers"*: `Metagenomic sequence name,Number of CDS,Number of annotated CDS,Number of associated KO,Number of associated PFAM` | |||
| > - {% icon param-file %} *"Data File (tab-delimted)"*: output of **Select last** {% icon tool %} | |||
| > - {% icon param-file %} *"Data File (tab-delimited)"*: output of **Select last** {% icon tool %} | |||
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I think we need to fix the upstream tool.
Is this tool needed or can we replace it with something from IUC?
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This tool is quite nice for directly adding a header to a file without creating a new one, and then combining both files tail-to-head. Would you happen to have another suggestion to do the same?
bgruening
reviewed
Dec 17, 2024
bgruening
reviewed
Dec 17, 2024
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This PR adds a new microbiome tutorial: "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data"