[DOC] add docs for flank.

docs/content/tools/flank.rst

 ###############
 *flank*
-###############
\ No newline at end of file
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/flank-glyph.png 
+    :width: 600pt 
+
+|
+
+``bedtools flank`` will create two new flanking intervals for each interval in 
+a BED/GFF/VCF file. Note that ``flank`` will restrict the created flanking
+intervals to the size of the chromosome  (i.e. no start < 0 and no end > 
+chromosome size).
+
+.. note::
+
+    In order to prevent creating intervals that violate chromosome boundaries,
+    ``bedtools flank`` requires a *genome* file defining the length of each 
+    chromosome or contig.
+
+.. seealso::
+
+    :doc:`../tools/slop`
+    
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+  bedtools flank [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
+
+**(or):**
+::
+
+  flankBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
+    
+===========================      ===============================================================================================================================================================================================================
+ Option                           Description
+===========================      ===============================================================================================================================================================================================================
+**-b**				             Increase the BED/GFF/VCF entry by the same number base pairs in each direction. *Integer*.							 
+**-l**					         The number of base pairs to subtract from the start coordinate. *Integer*.
+**-r**                           The number of base pairs to add to the end coordinate. *Integer*.
+**-s**                           Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the *end* coordinate.
+**-pct**                         Define -l and -r as a fraction of the feature's length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp "upstream".  Default = false.
+===========================      ===============================================================================================================================================================================================================
+
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, ``bedtools flank`` will either add a fixed number of bases in each 
+direction (``-b``) or an asymmetric number of bases in each direction 
+with ``-l`` and ``-r``.
+
+
+.. code-block:: bash
+
+  $ cat A.bed
+  chr1 100 200
+  chr1 500 600
+
+  $ cat my.genome
+  chr1 1000
+
+  $ bedtools flank -i A.bed -g my.genome -b 5
+  chr1	95	100
+  chr1	200	205
+  chr1	495	500
+  chr1	600	605
+
+  $ bedtools flank -i A.bed -g my.genome -l 2 -r 3
+  chr1	98	100
+  chr1	200	203
+  chr1	498	500
+  chr1	600	603
+  
+
+
+
+However, if the requested number of bases exceeds the boundaries of the 
+chromosome, ``bedtools flank`` will "clip" the feature accordingly.
+
+.. code-block:: bash
+
+  $ cat A.bed
+  chr1 100 200
+  chr1 500 600
+
+  $ cat my.genome
+  chr1 1000
+
+  $ bedtools flank -i A.bed -g my.genome -b 800
+  chr1	0	100
+  chr1	200	1000
+  chr1	0	500
+  chr1	600	1000
+
+
+==========================================================================
+``-pct`` Resizing features by a given fraction
+==========================================================================
+``bedtools flank`` will optionally create flanking intervals whose size is  
+user-specified fraction of the original interval.
+
+For example:
+
+.. code-block:: bash
+
+  $ cat A.bed
+  chr1 100 200
+  chr1 500 700
+  
+  ################################################################
+  # note the flanking intervals from the second record in A.bed
+  # are 20bp whereas the flanking intervals from the first record
+  # are only 10bp
+  ################################################################
+  $ bedtools flank -i A.bed -g my.genome -b 0.5 -pct
+  chr1	90	100
+  chr1	200	210
+  chr1	480	500
+  chr1	700	720
+
+
+

docs/content/tools/slop.rst

@@ -21,6 +21,9 @@ user-defined number of bases. While something like this could be done with an
     ``bedtools slop`` requires a *genome* file defining the length of each 
     chromosome or contig.
 
+.. seealso::
+
+    :doc:`../tools/flank`
 
 ==========================================================================
 Usage and option summary
@@ -33,7 +36,7 @@ Usage and option summary
 **(or):**
 ::
 
-  bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
+  slopBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
     
 ===========================      ===============================================================================================================================================================================================================
  Option                           Description
@@ -95,7 +98,7 @@ chromosome, ``bedtools slop`` will "clip" the feature accordingly.
 ==========================================================================
 ``-s`` Resizing features according to strand
 ==========================================================================
-**bedtools slop** will optionally increase the size of a feature based on strand.
+``bedtools slop`` will optionally increase the size of a feature based on strand.
 
 For example:
 
@@ -116,7 +119,7 @@ For example:
 ==========================================================================
 ``-pct`` Resizing features by a given fraction
 ==========================================================================
-**bedtools slop** will optionally increase the size of a feature by a 
+``bedtools slop`` will optionally increase the size of a feature by a 
 user-specific fraction.
 
 For example: