diff riboplot.xml @ 8:844eb8c36f32

Add help section in xml and update usage documentation

--- a/riboplot.xml	Thu Aug 13 15:03:20 2015 +0100
+++ b/riboplot.xml	Mon Aug 17 10:27:58 2015 +0100
@@ -50,5 +50,60 @@
         <data format="html" name="html_file" label="riboplot (HTML report)"/>
     </outputs>
     <help>
+**RiboPlot**
+
+Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM).
+
+----
+
+**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. 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)
+
     </help>
 </tool>