upd doc

doc/body.rst

@@ -4,7 +4,7 @@ Installation and running
 MAGERI is distributed in a form of executable JAR file and requires 
 `Java v1.8 <http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html>`__ to run. 
 Source code and binaries can be found in corresponding 
-`repository <https://github.com/mikessh/mageri>`__. Latest release can be found `here <https://github.com/mikessh/mageri/releases/latest>`__. 
+`repository <https://github.com/mikessh/mageri>`__. The latest release can be found `here <https://github.com/mikessh/mageri/releases/latest>`__. 
 MAGERI can be executed by running
 
 .. code-block:: bash
@@ -419,6 +419,9 @@ Advanced
 Presets
 ^^^^^^^
 
+Importing and exporting parameters
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
 By default MAGERI runs with pre-configured and optimized parameters, so change them 
 only if you know what you are doing. The parameter config can be changed by exporting, 
 modifying and re-importing corresponding XML file:
@@ -430,7 +433,8 @@ modifying and re-importing corresponding XML file:
    ...
    java -Xmx64G -jar mageri.jar --import-preset my_preset.xml [arguments]
    
-The content of the default XML config file is given below:
+Note that the ``--platform`` and ``--library-type`` arguments can be specified to alter the
+default preset. The content of the default XML config file is given below:
 
 .. code-block:: xml
 
@@ -532,6 +536,8 @@ Will have the following difference:
 Parameter descriptions
 ~~~~~~~~~~~~~~~~~~~~~~
 
+Below goes the description of each parameter that can be changed in configuration XML file.
+
 *Preset*
 
 - ``version`` version of software that generated this preset via ``--export-preset``.
@@ -608,12 +614,12 @@ The parameters you are likely to change under certain conditions:
 -  ``readLength`` when analyzing data generated by 454, IonTorrent platfroms and MiSeq long reads
 -  ``forceOverseq`` and ``defaultOverseq`` in case MIG size histogram shows irregular behavior or ``5+`` reads per UMI coverage cannot be reached
 -  ``mismatchPenalty``, ``minIdentityRatio`` and ``minAlignedQueryRelativeSpan`` in case of a complex library and high number of artefact alignments; Note that a good solution to this problem is to introduce additional references (e.g. pseudogenes) if your reference set doesn't cover everything that can be amplified with your primers
--  ``errorModelType` and ``substitutionErrorRateMatrix`` .. we plan to publish a comprehensive set of error models inferred for different polymerases
+-  ``errorModelType`` and ``substitutionErrorRateMatrix`` .. we plan to publish a comprehensive set of error models inferred for different polymerases
 
 Batch processing
 ^^^^^^^^^^^^^^^^
 
-MAGERI can be configured to run for multiple input files using a flexible JSON metadata config.
+MAGERI can be configured to run for multiple input files using a metadata config in JSON format.
 An example of metadata file is given below:
 
 .. code-block:: json