From eb716944ab73d33fb2d2de0a808dcd33c170bf49 Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Tue, 28 Jan 2025 13:58:51 -0500 Subject: [PATCH] Updated QuickStart EukPhylo (markdown) --- QuickStart-EukPhylo.md | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/QuickStart-EukPhylo.md b/QuickStart-EukPhylo.md index 9751c14..6c90e65 100644 --- a/QuickStart-EukPhylo.md +++ b/QuickStart-EukPhylo.md @@ -50,14 +50,14 @@ 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 ``` -Here add detail of each option possible: -* -1 = start script -* -2 = end script -* --assembled_transcripts = Folder with Assembled transcripts in fasta format -* -o = path to output folder +Code flags: +* -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 +* -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 @@ -85,10 +85,10 @@ To add the XPC option, only available for transcriptomes, user need to add the - ``` python wrapper.py -1 1 -2 5 --cds CDS -o Output_Folder --genetic_code Gcodes.txt -d Databases > log.txt ``` -Here add detail of each options possible: -* -1 = start script -* -2 = end script -* --cds = Folder with CDS files in fasta format +Code flags: +* -1 = start/first script to run. +* -2 = end/last script to run. +* --cds = path to folder with CDS files 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