view plot_rna.xml @ 24:431aebd93843 draft default tip

Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.

<tool id="rna_probing_plot" version="1.0.0" name="RNA Plot" force_history_refresh="True">

    <description></description>
    <requirements>
        <requirement type="package" version="3.1.1">R_3_1_1</requirement>
        <requirement type="R-module">RNAprobR</requirement>
        <requirement type="package" version="1.0.0">RNAprobR</requirement>
        <requirement type="set_environment">RNA_PROBING_SCRIPT_PATH</requirement>
    </requirements>

    <command interpreter="Rscript">
        plot_rna.R -i $input -t "$transcript" -m $norm_method -c $cutoff -p $plot_type -o $plot > /dev/null
    </command>

    <inputs>
        <param name="input" type="data" format="tabular" label="Input dataset" help="'Normalize' tool tabular output." />

        <param name="transcript" type="text" size="20" label="Transcript identifier" help="Select the transcript that the plot should be generated for.">
            <validator type="empty_field"/>
        </param>
        <param name="norm_method" type="select" display="checkboxes" multiple="true" label="Normalization method" help="Column values to be ploted (One plot per selected method).">
            <option value="dtcr">deltaTCR</option>
            <option value="slograt">Smooth Log2 Ratio</option>
            <option value="swinsor">Sliding window Winsorization</option>
            <option value="TC.treated">Termination Count (Treated)</option>
            <option value="Cover.treated">Coverage (Treated)</option>
            <option value="TCR.treated">TCR (Treated)</option>
            <option value="TC.control">Termination Count (Control)</option>
            <option value="Cover.control">Coverage (Control)</option>
            <option value="TCR.control">TCR (Control)</option>
        </param>
        <param name="cutoff" type="float" max="1.0" value="0.05" label="Significance level" help="Reports p-values or standard deviation (red asterisks) below the significance level. Set a negative value to print none." />
        <param name="plot_type" type="select" label="Plot type">
            <option value="l">Lines</option>
            <option value="h">Histogram</option>
        </param>
    </inputs>

    <outputs>
        <data name="plot" format="pdf" label="${tool.name} on ${on_string}: ${transcript} plot" />
    </outputs>

    <tests>
        <test>
        </test>
    </tests>

    <help>
**What it does**

Produces plots for a given transcript in the tabular file produced by *Normalize* tool (one plot per selected method). If a selected normalizing method is not included in the input file it simply not be plotted.

------

**Example**

Input (head)::

    RNAid           Pos nt  dtcr                    dtcr.p
    16S_rRNA_E.coli 1   A   0                       0.00787957002462928
    16S_rRNA_E.coli 2   A   0.000606618229204106    2.87738710042044e-07
    16S_rRNA_E.coli 3   A   0.00170457733442839     0.0242502062681708
    16S_rRNA_E.coli 4   T   0.00171914631528914     0.504983784068465
    16S_rRNA_E.coli 5   T   0.00111252808608504     5.26073688354678e-06
    16S_rRNA_E.coli 6   G   0.00175507669063296     9.92896700324683e-05

Output (Significance: 1e-08, type: histogram)

.. image:: http://people.binf.ku.dk/slm279/plot.png

    </help>
</tool>