improve doc

doc/source/introduction.rst

@@ -50,7 +50,7 @@ matching.
 
 **Does it work ?**
 
-Yes! The estimated sensitivity is 61% on average with the default option and goes up to 88% with the `--local_max` option. The missing *attC* sites are usually at the end of the array.  The False positive rate with the `--local_max` option is estimated between 0.03 False Positive per Megabases (FP/Mb) to 0.72 FP/Mb. This leads to a probability of finding 2 consecutive *attC* sites within 4kb between 4.10^-6 and 7.10^-9. Finally, this parameters do not depend on the G+C percent of the given replicon.
+Yes! The estimated sensitivity is 61% on average with the default option and goes up to 88% with the ``--local_max`` option. The missing *attC* sites are usually at the end of the array.  The False positive rate with the ``--local_max`` option is estimated between 0.03 False Positive per Megabases (FP/Mb) to 0.72 FP/Mb. This leads to a probability of finding 2 consecutive *attC* sites within 4kb between 4.10^-6 and 7.10^-9. Finally, this parameters do not depend on the G+C percent of the given replicon.
 
 |benchmark|
 

doc/source/tutorial.rst

@@ -93,9 +93,21 @@ INFERNAL::
 
 Default is 1.
 
+Circularity
+-----------
+
+By default, IntegronFinder assumes your replicon to be circular. However, if they aren't, or if it's PCR fragments or contigs, you can specify that it's a linear fragment::
+
+    integron_finder mylinearsequence.fst --linear
+
+However, if ``--linear`` is not used and the replicon is smaller than ``4 x dt``
+(where ``dt`` is the distance threshold, so 4kb by default), the replicon is
+considered linear to avoid clustering problem
+
+
 .. _advance:
 
-Advanced use
+Advanced options
 ============
 
 .. _distance_threshold:
@@ -118,6 +130,10 @@ or, equivalently::
 
 This sets the threshold for clustering to 10 kb.
 
+.. note::
+    The option ``--outdir`` allows you to chose the location of the Results folder (``Results_Integron_Finder_mysequence``). If this folder already exists, IntegronFinder will not re-run analyses already done, except functional annotation. It allows you to re-run rapidly IntegronFinder with a different ``--distance_threshold`` value. Functional annotation needs to re-run each time because depending on the aggregation parameters, the proteins associated with an integron might change. 
+
+
 *attC* evalue
 -------------
 
@@ -129,19 +145,6 @@ to the cost of a much higher false positive rate.
 
     integron_finder mysequence.fst --evalue_attc 5
 
-Circularity
------------
-
-By default, IntegronFinder assumes replicon to be circular. However, if they
-aren't, or if it's PCR fragments or contigs, you can specify that it's a linear
-fragment::
-
-    integron_finder mylinearsequence.fst --linear
-
-However, if ``--linear`` is not used and the replicon is smaller than ``4 x dt``
-(where ``dt`` is the distance threshold, so 4kb by default), the replicon is
-considered linear to avoid clustering problem
-
 Palindromes
 -----------
 

integron_finder

@@ -1386,7 +1386,7 @@ Python {1}
  - citation:
      Automatic and accurate identification of integrons
      and cassette arrays in bacterial genomes reveals unexpected patterns
-     Jean Cury, Thomas Jové, Marie Touchon, Bertrand Néron, Eduardo PC Rocha 
+     Jean Cury, Thomas Jové, Marie Touchon, Bertrand Néron, Eduardo PC Rocha
      bioRxiv doi: http://dx.doi.org/10.1101/030866
  """.format(version, sys.version)
         return version_text