<tool id="riboseqr_triplet_periodicity" name="Triplet Periodicity"
      version="0.4.0">
    <description>
        (Step 2) Plot triplet periodicity for different read lengths.
    </description>
    <requirements>
        <requirement type="R-module">riboSeqR</requirement>
    </requirements>
    <command interpreter="python">riboseqr/triplet.py
        --rdata_load "$rdata_load"
        --fasta_file "$fasta_file"
        --start_codons "$start_codons"
        --stop_codons "$stop_codons"
        --include_lengths "$include_lengths"
        --analyze_plot_lengths "$analyze_plot_lengths"
        --text_legend "$text_legend"
        --rdata_save "$rdata_save"
        --html_file "$html_file"
        --output_path "$html_file.files_path"
    </command>
    <inputs>
        <param name="rdata_load" type="data" format="rda"
               label="Select prepared riboSeqR input (R data file)"
               multiple="false" optional="false"
               help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;findCDS
           parameters&lt;/font&gt;&lt;/h4&gt;">
            <validator type="expression"
                       message="Please check if the correct RDA file is selected">value.name == "Prepare riboSeqR input (R data file)"</validator>
        </param>

        <param format="fasta" name="fasta_file" type="data"
               label="Select FASTA file of the reference transcriptome"
               help="This Fasta file is used to find start (ATG) and
           stop codons(TAG, TAA, TGA) in frame with one another. If no files
           are listed, you will need to upload a FASTA file of the reference
           transcriptome.">
            <validator type="empty_field" message="Field requires a value"/>
        </param>

        <param name="start_codons" type="text" size="15" value="ATG"
               label="Start codon(s) to use"
               help="Default is ATG. Multiple values must be comma-separated.">
            <validator type="empty_field" message="Field requires a value"/>
        </param>

        <param name="stop_codons" type="text" size="15" value="TAG, TAA, TGA"
               label="Stop codon(s) to use"
               help="Default is TAG, TAA, TGA. Multiple values must be comma-separated.
             &lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;frameCounting
             parameters&lt;/font&gt;&lt;/h4&gt;">
            <validator type="empty_field" message="Field requires a value"/>
        </param>

        <param name="include_lengths" type="text"
               label="Lengths of ribosome footprints
             to be included"
               help="Here, you can specify the lengths of ribosome footprints to
             be included in the riboData object. &lt;br&gt;For example 25:30.
             Range, semi-colon separated. &lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;readingFrame
             parameters&lt;/font&gt;&lt;/h4&gt;" value="25:30"/>

        <param name="analyze_plot_lengths" type="text"
               label="Lengths of reads to be analysed for frame-shift, or to be plotted"
               help="[Optional] If omitted, all lengths will be plotted.
             &lt;br&gt;For example 26:30. Range, semi-colon separated.
             &lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;plotFS
             parameters&lt;/font&gt;&lt;/h4&gt;" value="26:30"/>

        <param name="text_legend" type="text" size="30"
               value='Frame 0, Frame 1, Frame 2'
               label="Text for legend used in the
             plot" help="Comma-separated values."/>
    </inputs>
    <outputs>
        <data format="rda" name="rdata_save"
              label="Triplet periodicity (R data file)"/>
        <data format="html" name="html_file"
              label="Triplet periodicity (HTML report)"/>
    </outputs>
    <tests>
        <test>
            <param name="rdata_load" value="Prepare riboSeqR input (R data file)" ftype="rda"/>
            <param name="fasta_file" value="zebrafish.fasta.bz2" />
            <param name="include_lengths" value="25:30" />
            <param name="analyze_plot_lengths" value="26:30" />
            <output name="html_file" file="Triplet_periodicity_(HTML_report).html">
                <extra_files type="file" name="Periodicity-plot.png" value="Periodicity-plot.png" ftype="png"/>
                <extra_files type="file" name="Periodicity-plot.pdf" value="Periodicity-plot.pdf" ftype="pdf"/>
            </output>
        </test>
    </tests>
    <help>
About
-----
This tool can be used to plot triplet periodicity for different read lengths.
The inputs for this program are

#. Prepare riboSeqR input (R data file) from the previous step.
#. FASTA format file of the reference transcriptome.

riboSeqR version: **1.0.4**.

How to use?
-----------
Inputs
......
Select prepared R data file from the previous step.

Select FASTA format file of the reference transcriptome, review/change other
options if necessary and execute program.

Outputs
.......
The following files will be generated on completion:

#. Triplet periodicity (HTML report)

   A HTML file with results and links to other output files - triplet
   periodicity plot (PDF) and R script used for the session.

#. Triplet periodicity (R data file)

   Used as input for the next step - *Metagene analysis*.

riboSeqR functions used
.......................
findCDS, frameCounting, readingFrame and plotFS.

For detailed description of the functions and the options used, please consult
the riboSeqR documentation.

Links
.....
* `Bioconductor package information on riboSeqR`__
* riboSeqR - `Reference manual`_
* riboSeqR - `Introduction and workflow example`_

.. _riboSeqR: http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html

__ riboSeqR_

.. _manual: http://bioconductor.org/packages/3.0/bioc/manuals/riboSeqR/man/riboSeqR.pdf

.. _`Reference manual`: manual_

.. _documentation: http://bioconductor.org/packages/3.0/bioc/vignettes/riboSeqR/inst/doc/riboSeqR.pdf

.. _`Introduction and workflow example`: documentation_

    </help>
</tool>