<tool id="Annotation visualization" name="GIN visualizator" version="1.0.0">
  <description>of peaks distribution</description>
  <command interpreter="python">TSS_distance.py $input $out_file1 $numerical_column "$title" $window $breaks $density</command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Dataset" help="Query missing? See TIP below"/>
    <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
    <param name="breaks" type="integer" size="4" value="20" label="Number of breaks (bars)"/>
    <param name="title" type="text" size="30" value="Histogram" label="Plot title"/>
    <param name="window" type="integer" size="10" value="4000" label="Zoom visualitazion"/>
    <param name="density" type="boolean" checked="yes" label="Include smoothed density"/>
  </inputs>
  <outputs>
    <data format="pdf" name="out_file1" />
  </outputs>
  <help>
  
.. class:: infomark

**What it does**

This tool generates a distribution of peaks with respect to their distance from TSS.

PLEASE, for more detailed information refer to the CARPET user Manual:
click to download_ it.

.. _download: /static/example_file/CARPET_userManual.zip

-----

.. class:: warningmark

This tool requires at least 1 numerical column **"distance from TSS"**.

-----

**Syntax**

- All invalid, blank and comment lines in the query are skipped.  The number of skipped lines is displayed in the resulting history item.
- **Numerical column for x axis** - only numerical columns are possible.
- **Number of breaks(bars)** - breakpoints between histogram cells. Value of '0' will determine breaks automatically.
- **Plot title** - the histogram title.
- **Label for x axis** - the label of the x axis for the histogram.
- **Zoom visualization** - Limit of the X axis. All the peaks falling beyond this limit are plotted in the last histogram cell. 
- **Include smoothed density** - if checked, the resulting graph will join the given corresponding points with line segments.

-----

**Example**

- Input dataset ann_file from GIN (twelve columns: c1, c2, c3, c4, c5... c12):

.. image:: static/images/CARPET/output_ann.png


- Chose column **c12** ("Distance TSS"). 
   
.. image:: static/images/CARPET/hist_ann.png

</help>
</tool>

