diff docs/usage.rst @ 8:844eb8c36f32

Add help section in xml and update usage documentation

--- a/docs/usage.rst	Thu Aug 13 15:03:20 2015 +0100
+++ b/docs/usage.rst	Mon Aug 17 10:27:58 2015 +0100
@@ -8,9 +8,165 @@
 
 Parameters
 ..........
-1. Ribo-Seq alignment file (sorted BAM)
-   A bowtie 1 
+1. Ribo-Seq alignment file (Sorted BAM file)
+
+   A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
+   file should be sorted. This can be done using one of the following methods.
+
+   1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
+   2. ``samtools sort input.bam inputsorted``
+
+2. Transcriptome (FASTA)
+
+   A FASTA format file with sequences of the transcripts.
+
+3. Name of the transcript to plot (Text)
+
+   The name of the transcript to plot **should** match the name in the transcriptome (FASTA)
+   and the Ribo-Seq/RNA-Seq alignment (BAM).
+
+4. RNA coverage [optional] (Sorted BAM file)
+
+   If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage.
+
+5. Read lengths to consider [Optional] (Integer - 0 or greater)
+
+   If this option is provided, only Ribo-Seq data of the given length is considered.
+
+6. Offset [optional] (Integer - 0 or greater)
+
+   If this option is provided, this offset is added to the read alignment positions.
+
+Output
+......
+1. Plots (PNG and SVG)
+
+   Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue)
+
+   RNA coverage as a gray background (if the RNA coverage option was selected).
+
+   The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames.
+
+   The color codes are start (white) and stop (dark gray).
+
+   .. image:: ../images/riboplot.png
+
+2. RiboSeq read counts in 3 frames for each position in the transcript (CSV)
+
+
+Command line
+............
+``riboplot`` can also be run on the command line. The usage is ::
+
+    usage: python riboplot.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT
+                    [-n RNA_FILE] [-l INTEGER] [-s INTEGER] [-m HTML_FILE]
+                    [-o OUTPUT_PATH] [-d]
+
+    Plot and output read counts for a single transcript
+
+    optional arguments:
+    -h, --help
+        show this help message and exit
+
+    -n RNA_FILE, --rna_file RNA_FILE
+        RNA-Seq alignment file (BAM)
+
+    -l INTEGER, --read_length INTEGER
+        Read length to consider (default: None)
+
+    -s INTEGER, --read_offset INTEGER
+        Read offset (default: 0)
+
+    -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
 
 RiboCount
 ---------
+Output read counts for all transcripts in an alignment.
 
+Parameters
+..........
+1. Ribo-Seq alignment file (Sorted BAM file)
+
+   A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
+   file should be sorted. This can be done using one of the following methods.
+
+   1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
+   2. ``samtools sort input.bam inputsorted``
+
+2. Transcriptome (FASTA)
+
+   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.
+
+4. Offset [optional] (Integer - 0 or greater)
+
+   If this option is provided, this offset is added to the read alignment positions.
+
+Output
+......
+Read counts for all transcripts in the alignment (ZIP)
+
+The output file ``ribocount_output.zip`` should first be uncompressed. This will generate
+a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount.
+
+Total reads for each transcript will be displayed in a table along with the name of the transcript and a link
+to the CSV file containing the read counts in 3 frames for each position in the transcript.
+
+.. image:: ../images/ribocount.png
+
+Command line
+............
+``ribocount`` can also be run on the command line. The usage is ::
+
+    usage: python ribocount.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER]
+    [-s INTEGER] [-m HTML_FILE] [-o OUTPUT_PATH] [-d]
+
+    Output read counts for all transcripts
+
+    optional arguments:
+
+        -h, --help            show this help message and exit
+
+        -l INTEGER, --read_length INTEGER
+            Read length to consider (default: None)
+
+        -s INTEGER, --read_offset INTEGER
+            Read offset (default: 0)
+
+        -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
+