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Updated PhyloToL Part 2 (markdown)

Katzlab 2024-08-09 17:38:25 -04:00
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PhyloToL-Part-2.md

@ -26,6 +26,13 @@ You will also need to create a 'rules' file. The format here varies between the
## Running
To run the CL, use a similar command structure as described for running PhyloToL part 2 above, and add the `--contamination_loop` parameter to activate the contamination loop and specify a mode and the path to a rules file. Available parameters are:
| Parameter | required | Options | Description | default |
| ------------- | ------------- | ------------- | ------------- | ------------- |
| --contamination_loop | yes | seq, clade | The mode in which to run the loop | none |
| --nloops | no | _int_ | Number of iterations | 5 |