<tool id="riboseqr_ribosome_profile" name="Plot Ribosome Profile"
      version="0.4.0">
    <description>
        (Step 4) Plot Ribosome profile using riboSeqR.
    </description>
    <requirements>
        <requirement type="R-module">riboSeqR</requirement>
    </requirements>
    <command interpreter="python">riboseqr/ribosome_profile.py
        --rdata_load "$rdata_load"
        --transcript_name "$transcript_name"
        --transcript_length "$transcript_length"
        --transcript_cap "$transcript_cap"
        --html_file "$html_file"
        --output_path "$html_file.files_path"
    </command>
    <inputs>
        <param name="rdata_load" format="rda" type="data"
               label="Select Metagene analysis (R data file)"
               multiple="false">
            <validator type="expression"
                       message="Please check if the correct RDA file is selected">value.name == "Metagene analysis (R data file)"</validator>
        </param>

        <param name="transcript_name" type="text" size="30"
               label="Name of the transcript to be plotted"
               help="Plot of ribosome footprint abundance and mRNA coverage
               (if available) for a specific transcript.">
            <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
            <validator type="empty_field" message="Field requires a value"/>
            <sanitizer>
                <valid>
                    <add value="|"/>
                </valid>
            </sanitizer>
        </param>

        <param name="transcript_length" type="text"
               label="Select Ribosome footprint length"
               help="" value="28">
            <validator type="expression" message="Please input a single footprint length">len(value.split(',')) == 1</validator>
            <validator type="expression" message="Please input a single footprint length">len(value.split(' ')) == 1</validator>
            <validator type="empty_field" message="Field requires a value"/>
        </param>

        <param name="transcript_cap" type="integer" value="200"
               label="Cap on the largest value that will be plotted as an
               abundance of the ribosome footprint data"/>
    </inputs>
    <outputs>
        <data format="html" name="html_file"
              label="Plot ribosome profile (HTML report)"/>
    </outputs>
    <tests>
        <test>
            <param name="rdata_load" value="Metagene analysis (R data file)" />
            <param name="transcript_name" value="gi|31340752|ref|NM_178437.2|" />
            <param name="transcript_length" value="28" />
            <param name="transcript_cap" value="200" />
            <output name="html_file" file="Plot_ribosome_profile_(HTML_report).html">
              <extra_files type="file" name="Ribosome-profile-plot.png" value="Ribosome-profile-plot.png" ftype="png" />
              <extra_files type="file" name="Ribosome-profile-plot.pdf" value="Ribosome-profile-plot.pdf" ftype="pdf" />
            </output>
        </test>
    </tests>
    <requirements>
        <requirement type="R-module">riboSeqR</requirement>
    </requirements>
    <help>
About
-----
This tool can be used for generating a ribosome profile plot for a given
transcript. The input is the R data file from the previous
step - Metagene analysis.

riboSeqR version: **1.0.4**.

How to use?
-----------
Inputs
......
Select **Metagene analysis (R data file)** from the previous step, enter name
of the transcript to plot, review/change parameters and execute program.

.. class:: warningmark

        The transcript name should correspond to names used in SAM alignments
        and FASTA file of the transcriptome.

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

Plot ribosome profile (HTML report)

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

riboSeqR functions used
.......................
plotTranscript.

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>