view tools/plotting/bar_chart.xml @ 1:cdcb0ce84a1b

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<tool id="barchart_gnuplot" name="Bar chart">
  <description>for multiple columns</description>
  <command interpreter="python">
    #if $xtic.userSpecified == "Yes" #bar_chart.py $input $xtic.xticColumn $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size"
    #else                            #bar_chart.py $input 0 $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size"
    #end if
  </command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
    <conditional name="xtic">
        <param name="userSpecified" type="select" label="Use X Tick labels?" help="see example below">
            <option value="Yes">Yes</option>
            <option value="No">No</option>
        </param>
        <when value="Yes">
            <param name="xticColumn" type="data_column" data_ref="input" numerical="False" label="Use this column for X Tick labels" />
        </when>
        <when value="No">
        </when>
    </conditional>           
    <param name="colList" label="Numerical columns" type="data_column" numerical="True" multiple="True" data_ref="input" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
    <param name="title" type="text" size="30" value="Bar Chart" label="Plot title"/>
    <param name="ylabel" type="text" size="30" value="V1" label="Label for Y axis"/>
    <param name="ymin" type="integer" size="4" value="0" label="Minimal value on Y axis" help="set to 0 for autoscaling"/>
    <param name="ymax" type="integer" size="4" value="0" label="Maximal value on Y axis" help="set to 0 for autoscaling"/>
    <param name="pdf_size" type="select" label="Choose chart size (pixels)">
        <option value="800,600">Normal: 800 by 600</option>
        <option value="640,480">Small: 640 by 480</option>
        <option value="1480,800">Large: 1480 by 800</option>
        <option value="600,800">Normal Flipped: 600 by 800</option>
        <option value="480,640">Small Flipped: 480 by 640</option>
        <option value="800,1480">Large Flipped: 800 by 1480</option>
    </param>
  </inputs>
  <outputs>
    <data format="png" name="out_file1" />
  </outputs>
  <requirements>
    <requirement type="python-module">Gnuplot</requirement>
    <requirement type="python-module">Numeric</requirement>
  </requirements>
  <help>

**What it does**

This tool builds a bar chart on one or more columns. Suppose you have dataset like this one::

  Gene1	10	15
  Gene2	20	14
  Gene3	67	45
  Gene4	55	12

Graphing columns 2 and 3 while using column 1 for X Tick Labels will produce the following plot:

.. image:: ./static/images/bar_chart.png 
   :height: 324 
   :width: 540 
    
</help>
</tool>