diff ribocount.xml @ 8:844eb8c36f32

Add help section in xml and update usage documentation

--- a/ribocount.xml	Thu Aug 13 15:03:20 2015 +0100
+++ b/ribocount.xml	Mon Aug 17 10:27:58 2015 +0100
@@ -26,5 +26,47 @@
         <data format="html" name="html_file" label="ribocount (HTML report)"/>
     </outputs>
     <help>
+**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
+
     </help>
 </tool>