Added Cami Opal - A tool for evaluating taxonomic metagenome profilers #6096
Conversation
There was a problem hiding this comment.
Some comments inline.
Out of interest: What is the difference or connection to https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber
amber is the cami binning evaluation tool (you need to provide a gold standard bin assignment / and optionally taxonomy for each bin) - so for DAS TOOL or other binners, opal is the cami evaluation tool for taxonomic composition - so Kraken2 / MetaPhlan ... in theory OPAL should also work for amplicon data (in terms of taxonomic assignment benchmarking) ... another thing to look into .... |
|
I apologize for the confusion caused by the multiple commits in this pull request. I have addressed the issues and made the necessary adjustments to the code. Please take another look and provide any further feedback. Thank you for your assistance! Best regards |
tools/cami-opal/cami_opal.xml
Outdated
| <param argument="--time" type="text" value="" optional="true" | ||
| label="Comma-separated runtimes in hours" | ||
| help="Comma-separated runtimes in hours" /> | ||
| <param argument="--memory" type="text" value="" optional="true" | ||
| label="Comma-separated memory usages in gigabytes" | ||
| help="Comma-separated memory usages in gigabytes" /> |
There was a problem hiding this comment.
I would allow adding it as optional, one could get this info from galaxy and add manually
|
Can you add one test with multiple samples as input ? |
| ## Copy the results to the specified output folder | ||
| && mkdir '$htmlreport.extra_files_path' | ||
| && cp output/results.html $htmlreport | ||
| && cp -r output/* '$htmlreport.extra_files_path' |
There was a problem hiding this comment.
Do all output files needs to be in this folder or only a handful that are part of the HTML?
There was a problem hiding this comment.
Most files should remain, as I haven't tested which ones are essential and which can be removed. So, I would recommend that you keep all of them in the folder for now.
There was a problem hiding this comment.
I checked the detailed examples form: Here - they are approximately 20 MB.
Tool details for Cami Opal
Checklist for submission
FOR CONTRIBUTOR:
I look forward to any feedback and thank you for your consideration.