Versión command line

README.md

@@ -1,5 +1,55 @@
-# maldisoft
+# Initial Maldisoft cmdline usage tutorial
 
-Moving the source to a public repository
-asa
+If you are reading this is because you already unpacked the program.
+
+If you list the files and directories you will find the directories:
+
+```
+data
+html
+```
+
+In the data directory you **MUST** create a sub directory with the data that you want to analyze together and then create a directory inside html where the results will be written.
+
+For instance for the NIH example:
+```
+mkdir data/nih
+mkdir html/nih
+```
+
+Copy inside `data/nih` the data to be analyzed.
+
+The list of peaks that you want to analyze is inside the file peaks.txt.  If you want to remove or add a new peak just follow the same format that is inside the file.  
+
+Currently:
+
+```
+1257.4
+1419.5
+1581.5
+1743.6
+1809.7
+1905.6
+```
+
+To run the program you just need to follow the following syntax in the terminal:
+
+```
+python maldisoft.py peaks.txt html/sample_name/ data/sample_name/*
+```
+
+For the NIH example it would be:
+```
+python maldisoft.py peaks.txt html/nih/ data/nih/*
+```
+
+The results should be inside `html/nih`.
+
+To open the results page in your computer go to the directory and double click the index.html file.
+
+If you have a mac just do:
+
+```
+open html/nih/index.html
+```