continue README for tool descriptions

tools/README.md

@@ -9,10 +9,13 @@ example file (usually containing default parameters that are set up on the `.rul
 
 All Snakemake tool descriptions try to respect some rules and best practices in their design:
 
-* First part correspond to all options that are set up from a `config.yaml` file
+* First part correspond to all options that are set up from a `config.yaml` file. They all have the nomenclature `__TOOLNAME_variable`.
 * Then the tool itself is described with:
   * input with the nomenclature: `__TOOLNAME_input`
   * output with the nomenclature: ` __TOOLNAME_output`
   * params with different options that are described above
+  	* There is usually a `exec_command` to give the possibility to change the way the tool is called (locally installed, singularity ...)
+  	* There is usually a `options` to specify all other command line options
+  * the shell command
 
 input and output are then set up in the Snakemake file that refer to the rule.
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