From 50064d71b65d140ab88e22b489e67482c330dc2b Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Tue, 28 Jan 2025 14:09:17 -0500 Subject: [PATCH] Updated QuickStart EukPhylo (markdown) --- QuickStart-EukPhylo.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/QuickStart-EukPhylo.md b/QuickStart-EukPhylo.md index 7b01cb0..0994796 100644 --- a/QuickStart-EukPhylo.md +++ b/QuickStart-EukPhylo.md @@ -50,15 +50,16 @@ EukPhylo part 1 runs CDS (genome) or assembled transcripts (transcriptome) throu ``` python wrapper.py -1 1 -2 7 --assembled_transcripts AssembledTranscripts -o Output_Folder --genetic_code Universal -d Databases > log.txt ``` +Code parameters: | Parameter | Description| | ----------- |----------------- | -| -1 | start/first script to run.| -| -2 | end/last script to run.| -| --assembled_transcripts | path to folder with Assembled transcripts in fasta format.| -| -o | path to output folder.| -| --genetic_code | specified genetic code, name of .txt file with Genetic codes; optional.| -| -d | path to Databases folder.| -| > log.txt | if added to the end of the command, it will output a log file with progress, warning, or error messages.| +| -1 | Start/first script to run.| +| -2 | End/last script to run.| +|--assembled_transcripts | Path to folder with Assembled transcripts in fasta format.| +| -o | Path to output folder.| +| --genetic_code | Specified genetic code, name of .txt file with Genetic codes; optional.| +| -d | Path to Databases folder.| +| > log.txt | If added to the end of the command, it will output a log file with progress, warning, or error messages.| ### Output: > ReadyToGo files = AA, NTD