[DOCS] updated slop docs

docs/content/tools/slop.rst

 ###############
 *slop*
 ###############
-**slopBed** will increase the size of each feature in a feature file be a user-defined number of bases. While
-something like this could be done with an "**awk '{OFS="\t" print $1,$2-<slop>,$3+<slop>}'**",
-**slopBed** will restrict the resizing to the size of the chromosome (i.e. no start < 0 and no end >
-chromosome size).
+
+|
+
+.. image:: ../images/tool-glyphs/intersect-glyph.png 
+    :width: 600pt 
+
+|
+
+``bedtools slop`` will increase the size of each feature in a feature file be a 
+user-defined number of bases. While something like this could be done with an 
+``awk '{OFS="\t" print $1,$2-<slop>,$3+<slop>}'``,
+``bedtools slop`` will restrict the resizing to the size of the chromosome 
+(i.e. no start < 0 and no end > chromosome size).
+
+.. note::
+
+    In order to prevent the extension of intervals beyond chromosome boundaries,
+    ``bedtools slop`` requires a *genome* file defining the length of each 
+    chromosome or contig.
 
 
 ==========================================================================
 Usage and option summary
 ==========================================================================
-Usage:
+**Usage**:
 ::
-  slopBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
-  
+
+  bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
+
+**(or):**
+
+  bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
+    
 ===========================      ===============================================================================================================================================================================================================
  Option                           Description
 ===========================      ===============================================================================================================================================================================================================
@@ -21,6 +41,8 @@ Usage:
 **-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**                         
+**-header**                       
 ===========================      ===============================================================================================================================================================================================================
 
 
@@ -28,57 +50,92 @@ Usage:
 ==========================================================================
 Default behavior
 ==========================================================================
-By default, **slopBed** will either add a fixed number of bases in each direction (**-b**) or an asymmetric
-number of bases in each direction (**-l** and **-r**).
+By default, ``bedtools slop`` 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``.
 
-For example:
-::
-  cat A.bed
+
+.. code-block:: bash
+
+  $ cat A.bed
   chr1 5 100
   chr1 800 980
 
-  cat my.genome
+  $ cat my.genome
   chr1 1000
 
-  slopBed -i A.bed -g my.genome -b 5
+  $ bedtools slop -i A.bed -g my.genome -b 5
   chr1 0 105
   chr1 795 985
 
-  slopBed -i A.bed -g my.genome -l 2 -r 3
+  $ bedtools slop -i A.bed -g my.genome -l 2 -r 3
   chr1 3 103
   chr1 798 983
   
 
-However, if the requested number of bases exceeds the boundaries of the chromosome, **slopBed** will
-"clip" the feature accordingly.
-::
-  cat A.bed
+However, if the requested number of bases exceeds the boundaries of the 
+chromosome, ``bedtools slop`` will "clip" the feature accordingly.
+
+.. code-block:: bash
+
+  $ cat A.bed
   chr1  5   100
   chr1  800 980
 
-  cat my.genome
+  $ cat my.genome
   chr1  1000
 
-  slopBed -i A.bed -g my.genome -b 5000
+  $ bedtools slop -i A.bed -g my.genome -b 5000
   chr1  0   1000
   chr1  0   1000
 
   
   
 ==========================================================================
-Resizing features according to strand
+``-s`` Resizing features according to strand
 ==========================================================================
-**slopBed** 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:
-::
-  cat A.bed
+
+.. code-block:: bash
+
+  $ cat A.bed
   chr1 100 200 a1 1 +
   chr1 100 200 a2 2 -
 
-  cat my.genome
+  $ cat my.genome
   chr1 1000
 
-  slopBed  -i A.bed -g my.genome -l 50 -r 80 -s
+  $ bedtools slop  -i A.bed -g my.genome -l 50 -r 80 -s
   chr1 50  280 a1 1 +
   chr1 20  250 a2 2 -
+  
+  
+==========================================================================
+``-pct`` Resizing features by a given fraction
+==========================================================================
+**bedtools slop** will optionally increase the size of a feature by a 
+user-specific fraction.
+
+For example:
+
+.. code-block:: bash
+
+  $ cat A.bed
+  chr1 100 200 a1 1 +
+
+  $ bedtools slop -i A.bed -g my.genome -b 0.5 -pct
+  chr1 50  250 a1 1 +
+
+  $ bedtools slop -i a.bed -l 0.5 -r 0.0 -pct -g my.genome 
+  chr1	50	200	a1	1	+
+
+
+==========================================================================
+``-header`` Print the header for the A file before reporting results.
+==========================================================================
+By default, if your A file has a header, it is ignored when reporting results.
+This option will instead tell bedtools to first print the header for the
+A file prior to reporting results.
+