comparison riboplot.xml @ 8:844eb8c36f32

Add help section in xml and update usage documentation

7:096c6bbf4a04

    </inputs>
    <outputs>
        <data format="html" name="html_file" label="riboplot (HTML report)"/>
    </outputs>
    <help>
    </help>
</tool>

8:844eb8c36f32

    </inputs>
    <outputs>
        <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>