From e8742bd3f6ab679e35c8f209526c7f663a0e4d5b Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Tue, 28 Jan 2025 14:07:31 -0500 Subject: [PATCH] Updated QuickStart EukPhylo (markdown) --- QuickStart-EukPhylo.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/QuickStart-EukPhylo.md b/QuickStart-EukPhylo.md index 6c90e65..7b01cb0 100644 --- a/QuickStart-EukPhylo.md +++ b/QuickStart-EukPhylo.md @@ -50,14 +50,15 @@ 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 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. +| 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.| ### Output: > ReadyToGo files = AA, NTD