From 546c7747e6befb92ef9615d554c27385115d49ac Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Mon, 12 Aug 2024 15:16:50 -0400 Subject: [PATCH] Updated PhyloToL Part 1: GF assignment (markdown) --- PhyloToL-Part-1:-GF-assignment.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/PhyloToL-Part-1:-GF-assignment.md b/PhyloToL-Part-1:-GF-assignment.md index 528f550..61e926b 100644 --- a/PhyloToL-Part-1:-GF-assignment.md +++ b/PhyloToL-Part-1:-GF-assignment.md @@ -122,3 +122,13 @@ Role of each script * **Main inputs** : A folder containing the [CDS](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/TestData), a folder containing the Databases, and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/Scripts). * **Outputs** : ReadyToGo files (AA and NTD) and taxon summary. + +| Parameter | Type| Options| Description| +| ----------- | ----------------- | +| --first_script| int | 1, 2, 3, 4 | First script to run | +| --last_script | int | 2, 3, 4, 5 | First script to run| +| --cds| str|Path to a folder of nucleotide CDS| Each file name should start with a unique 10 digit code, and end in "_GenBankCDS.fasta", E.g. Op_me_hsap_GenBankCDS.fasta| +| --output| = str|Path for the output files | An "Output" folder will be created at this directory to contain all output files. By default this folder will be created at the parent directory of the Scripts folder | +| --genetic_code| str| Path to a file, Universal | If all of your taxa use the same genetic code, you may enter it here| +| --databases| str| Path to databases folder | The folder should contain all 3 databases| +