<tool id="riboseqr_metagene" name="Metagene Analysis" version="0.4.0">
    <description>
        (Step 3) Metagene analysis using riboSeqR.
    </description>
    <requirements>
        <requirement type="R-module">riboSeqR</requirement>
    </requirements>
    <command interpreter="python">riboseqr/metagene.py
        --rdata_load "$rdata_load"
        --selected_lengths "$selected_lengths"
        --selected_frames "$selected_frames"
        --hit_mean "$hit_mean"
        --unique_hit_mean "$unique_hit_mean"
        --ratio_check "$ratio_check"
        --plot_lengths "$plot_lengths"
        --min5p "$min5p"
        --max5p "$max5p"
        --min3p "$min3p"
        --max3p "$max3p"
        --cap "$cap"
        --plot_title "$plot_title"
        --rdata_save "$rdata_save"
        --html_file "$html_file"
        --output_path "$html_file.files_path"
    </command>
    <inputs>
        <param name="rdata_load" type="data" format="rda"
               label="Select Triplet periodicity (R data file)"
               multiple="false" optional="false"
               help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;filterHits parameters (footprint reads to be used in the analysis)&lt;/font&gt;&lt;/h4&gt;">
            <validator type="expression"
                       message="Please check if the correct RDA file is selected">value.name == "Triplet periodicity (R data file)"</validator>
        </param>

        <param name="selected_lengths" type="text" value="27"
               label="Length of ribosome footprint
               reads to be used in filtering (lengths)"
               help="ex: 27,28. Multiple values must be comma-separated.
               Please consult Periodicity-report.txt." optional="false">
            <validator type="empty_field" message="Field requires a value"/>
        </param>

        <param name="selected_frames" type="text" value=""
               label="Frames of the ribosome footprint reads to be used in filtering
               (frames)"
               help="ex: 1,0. Should be of equal length to the lengths parameter above.
               Multiple values must be comma-separated.
               Please consult the periodicity report from previous step."
               optional="false">
            <validator type="empty_field" message="Field requires a value"/>
        </param>

        <param name="hit_mean" size="4" type="integer" value="10"
               label="Mean number of hits within a replicate group that
               should be observed to pass filtering (hitMean)" optional="false">
            <validator type="empty_field" message="Field requires a value"/>
        </param>

        <param name="unique_hit_mean" size="4" type="integer" value="1"
               label="Mean number of unique sequences within a replicate group
               that should be observed to pass filtering
               (unqhitMean)" optional="false">
            <validator type="empty_field" message="Field requires a value"/>
        </param>

        <param name="ratio_check" type="boolean" checked="yes"
               label="Check the ratios of the expected phase to maximal phase
               within the putative coding sequence
               (ratioCheck)" falsevalue="FALSE"
               truevalue="TRUE"
               help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;plotCDS parameters&lt;/font&gt;&lt;/h4&gt;"/>

        <param name="plot_lengths" type="text"
               label="Length of footprints to be
               plotted (lengths)"
               help="Multiple values should be comma-separated.
               In that case, multiple plots will be produced" value="27"/>

        <param name="min5p" label="The distance upstream of the translation
        start to be plotted (min5p)" value="-20" type="integer"/>

        <param name="max5p" label="The distance downstream of the translation
        start to be plotted (max5p)" value="200" type="integer"/>

        <param name="min3p" label="The distance upstream of the translation
        end to be plotted (min3p)" value="-200" type="integer"/>

        <param name="max3p" label="The distance downtream of the translation
        end to be plotted (max3p)" value="20" type="integer"/>

        <param name="cap"
               label="If given, caps the height of plotted values (cap)"
               value="" type="integer" optional="true"/>

        <param name="plot_title"
               label="Title of the plot (main)" type="text" size="30"
               value=""/>
    </inputs>
    <outputs>
        <data format="rda" name="rdata_save"
              label="Metagene analysis (R data file)"/>
        <data format="html" name="html_file"
              label="Metagene analysis (HTML report)"/>
    </outputs>
    <tests>
        <test>
            <param name="rdata_load" value="Triplet periodicity (R data file)" ftype="rda"/>
            <param name="selected_lengths" value="28" />
            <param name="selected_frames" value="0" />
            <param name="plot_lengths" value="28" />
            <output name="html_file" file="Metagene_analysis_(HTML_report).html">
                <extra_files type="file" name="Metagene-analysis-plot1.png" value="Metagene-analysis-plot1.png"/>
                <extra_files type="file" name="Metagene-analysis-plot1.pdf" value="Metagene-analysis-plot1.pdf"/>
            </output>
        </test>
    </tests>
    <help>
About
-----
Metagene analysis using riboSeqR. The input is the R data file from the previous
step - Triplet periodicity.

riboSeqR version: **1.0.4**.

How to use?
-----------
Inputs
......
#. Select **Triplet periodicity (R data file)** from the previous step.

#. Specify length of ribosome footprint reads to be used in filtering
   (lengths). Only these reads **will** be used in the analysis.

#. Specify frames to consider. This information can be obtained
   from the **Triplet periodicity (HTML report)**.

   .. class:: warningmark

        Please note that the frames specified should correspond to the
        lengths of the reads.

#. Under **plotCDS parameters**, input length of footprints to be considered for
   generating the plot.

#. Review/change other options if necessary and execute program.

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

#. Metagene analysis (HTML report)

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

#. Metagene analysis (R data file)

   Used as input for the next step - *Plot Rribosome Profile*.

riboSeqR functions used
.......................
filterHits.

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>