From 1705349356ce22cec14c9abd35b80ec73c773f62 Mon Sep 17 00:00:00 2001
From: Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
Date: Thu, 10 Dec 2015 13:58:02 +0000
Subject: [PATCH] Update documentation

---
 docs/ribocount.rst | 36 ++++++++++++++++++++++++++++--------
 docs/riboplot.rst  | 38 ++++++++++++++++++++------------------
 2 files changed, 48 insertions(+), 26 deletions(-)

diff --git a/docs/ribocount.rst b/docs/ribocount.rst
index a60b8f6..ac91019 100644
--- a/docs/ribocount.rst
+++ b/docs/ribocount.rst
@@ -18,11 +18,15 @@ A FASTA format file with sequences of the transcripts.
 
 3. Read lengths to consider [optional] (Integer - 0 or greater)
 ...............................................................
-If this option is provided, only Ribo-Seq data of the given length is considered.
+If this option is provided, only Ribo-Seq data of the given read length is considered.
+Multiple read lengths can be provided and should be separated by commas. If multiple
+read lengths are input, corresponding read offsets should also be specified. If you
+do not wish to apply an offset, please input 0 for the corresponding offset.
 
-4. Offset [optional] (Integer - 0 or greater)
-.............................................
-If this option is provided, this offset is added to the read alignment positions.
+4. Read offset(s) corresponding to read lengths [optional] (Integer - 0 or greater)
+...................................................................................
+If this option is provided, this offset is added to the read alignment positions. Multiple
+offsets should be separated by commas.
 
 5. Restrict read counts
 .......................
@@ -47,30 +51,46 @@ Command line
 ------------
 ``ribocount`` can also be run on the command line. The usage is ::
 
-    ribocount [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER]
-                    [-s INTEGER] [-v | -r] [-m HTML_FILE] [-o OUTPUT_PATH]
-                    [-d]
+    ribocount.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l READ_LENGTHS]
+                 [-s READ_OFFSETS] [-v | -r] [-m HTML_FILE]
+                 [-o OUTPUT_PATH] [-d]
 
-    Output read counts for all transcripts
+Output read counts for all transcripts
 
 **required arguments**:
     -b RIBO_FILE, --ribo_file RIBO_FILE
         Ribo-Seq alignment file in BAM format
+
     -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA
         FASTA format file of the transcriptome
 
 **optional arguments**:
     -h, --help            show this help message and exit
+
+    -l READ_LENGTHS, --read_lengths READ_LENGTHS
+        Read lengths to consider (default: 0). Multiple read lengths should be
+        separated by commas. If multiple read lengths are specified, corresponding read offsets
+        should also be specified. If you do not wish to apply an offset, please input 0 for the corresponding read length
+
+    -s READ_OFFSETS, --read_offsets READ_OFFSETS
+        Read offsets (default: 0). Multiple read offsets should be separated by commas
+
     -l INTEGER, --read_length INTEGER
         Read length to consider (default: None)
+
     -s INTEGER, --read_offset INTEGER
         Read offset (default: 0)
+
     -v, --count_five      Flag. Output reads in 5' region
+
     -r, --count_three     Flag. Output reads in 3' region
+
     -m HTML_FILE, --html_file HTML_FILE
         Output file for results (HTML)
+
     -o OUTPUT_PATH, --output_path OUTPUT_PATH
         Files are saved in this directory
+
     -d, --debug           Flag. Produce debug output
 
 .. links
diff --git a/docs/riboplot.rst b/docs/riboplot.rst
index 024210f..49e940e 100644
--- a/docs/riboplot.rst
+++ b/docs/riboplot.rst
@@ -101,38 +101,40 @@ Command line
 
 Plot and output read counts for a single transcript
 
-optional arguments:
+**optional arguments:**
     -h, --help            show this help message and exit
 
     -n RNA_FILE, --rna_file RNA_FILE    RNA-Seq alignment file (BAM)
-    
-    -l READ_LENGTHS, --read_lengths READ_LENGTHS    
-        Read lengths to consider (default: 0). Multiple read lengths should be 
-        separated by commas. If multiple read lengths are specified, corresponding read offsets 
+
+    -l READ_LENGTHS, --read_lengths READ_LENGTHS
+        Read lengths to consider (default: 0). Multiple read lengths should be
+        separated by commas. If multiple read lengths are specified, corresponding read offsets
         should also be specified. If you do not wish to apply an offset, please input 0 for the corresponding read length
-    
+
     -s READ_OFFSETS, --read_offsets READ_OFFSETS
         Read offsets (default: 0). Multiple read offsets should be separated by commas
-    
-    -c one of default colorbrewer rgb greyorfs, --color_scheme one of default colorbrewer rgb greyorfs
-        Color scheme to use (default: default)
-    
+
+    -c COLOR_SCHEME, --color_scheme COLOR_SCHEME
+        One of default, colorbrewer, rgb, greyorfs
+
     -m HTML_FILE, --html_file HTML_FILE
         Output file for results (HTML)
-    
+
     -o OUTPUT_PATH, --output_path OUTPUT_PATH
         Files are saved in this directory
-    
+
     -d, --debug
         Flag. Produce debug output
 
-required arguments:
-    -b RIBO_FILE, --ribo_file RIBO_FILE Ribo-Seq alignment file in BAM format
-    
-    -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA FASTA format file of the transcriptome
-    
-    -t TEXT, --transcript_name TEXT Transcript name
+**required arguments:**
+    -b RIBO_FILE, --ribo_file RIBO_FILE
+        Ribo-Seq alignment file in BAM format
+
+    -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA
+        FASTA format file of the transcriptome
 
+    -t TEXT, --transcript_name TEXT
+        Transcript name
 
 .. links