Update Test_file_README.md

Test_files/Test_file_README.md

@@ -1,22 +1,58 @@
-Steps to test the MGSE3.1.py script with the test file are as follows:
+**Steps to test the MGSE3.py script:**
 
 git clone https://github.com/bpucker/MGSE
 
 cd Test_files
 
-You can find different input files and reference region files here. 
+There are three possible test cases for the script.
 
-Please read the script README for the usage of these different files.
+```
+Case 1) Testing with FASTA and FASTQ inputs:
 
-NOTE: 
+python3 MGSE3.py [--fasta <FASTA> --fastq <FASTQ> --seqtech ont]
+                 [--busco <BUSCO_TSV> | --gff <GFF3_FILE> | --all <ALL_POS>]
+                 --out <DIR>
 
-i) The fastq test file has long reads; If testing with this fastq file input, use minimap2 as the aligner.
+Case 2) Testing with bam file as input:
+
+python3 MGSE3.py [--bam <BAM> --bam_is_sorted]
+                 [--busco <BUSCO_TSV> | --gff <GFF3_FILE> | --all <ALL_POS>]
+                 --out <DIR>
+
+Case 3) Testing with coverage file as input:
+
+python3 MGSE3.py [--cov <COV>]
+                 [--busco <BUSCO_TSV> | --gff <GFF3_FILE> | --all <ALL_POS>]
+                 --out <DIR>
+```
+
+**Test files details:**
+
+FASTA     ->  Arabidopsis_thaliana.fa
+
+FASTQ     ->  Arabidopsis_thaliana.fq
+
+BAM       ->  Arabidopsis_thaliana.bam
+
+COV       ->  Arabidopsis_thaliana.cov
+
+BUSCO_TSV ->  Arabidopsis_thaliana_busco.tsv
+
+GFF3_FILE ->  Arabidopsis_thaliana.gff
+
+
+**More Information:** 
+
+i) The fastq test file has long reads (Oxford Nanopore Technology sequencing reads)
 
 ii) The .bam test file is already sorted.
 
-iii) The test files provided have content corresponding to the first 10^5 base pairs on chromosome 1 of
-Arabidopsis thaliana Col-0 accession.
+iii) The test files have information corresponding to the first 10^5 base pairs on chromosome 1 of
+    _Arabidopsis thaliana_ Col-0 accession. Hence you must get a genome size estimate of ~0.1 Mbp 
+    when testing MGSE3.1.py with these test files.
+
+**Note:**
 
-iv) You must get a genome size estimate of ~0.1 Mbp when testing MGSE3.1.py with these test files.
+For more details on the different parameters, please refer to the script README.