diff --git a/QuickStart-EukPhylo.md b/QuickStart-EukPhylo.md index 3054c0b..530cead 100644 --- a/QuickStart-EukPhylo.md +++ b/QuickStart-EukPhylo.md @@ -63,7 +63,6 @@ Code parameters: ### Output: 1. **ReadyToGo files = AA, NTD** - 2. **Summary and statistics of sequences** ### Modularity of options and replacing the Hook database @@ -87,19 +86,20 @@ 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 ``` -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 -* log.txt = if added to the end of the command, it will output a log file with progress, warning, or error messages +Code parameters: +| Parameter | Description| +| :--- |:--- | +| -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.| +|>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 - -> Summary and statistics of sequences +1. **ReadyToGo files = AA, NTD** +2. **Summary and statistics of sequences** ### Modularity of options and replacing the Hook database EukPhylo part 1 for genomes is composed of 5 scripts. User can choose to start or stop at each step by changing the -1 and/or -2 options.