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/tools/plotting/bar_chart.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="barchart_gnuplot" name="Bar chart">
 2  <description>for multiple columns</description>
 3  <command interpreter="python">
 4    #if $xtic.userSpecified == "Yes" #bar_chart.py $input $xtic.xticColumn $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size"
 5    #else                            #bar_chart.py $input 0 $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size"
 6    #end if
 7  </command>
 8  <inputs>
 9    <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
10    <conditional name="xtic">
11        <param name="userSpecified" type="select" label="Use X Tick labels?" help="see example below">
12            <option value="Yes">Yes</option>
13            <option value="No">No</option>
14        </param>
15        <when value="Yes">
16            <param name="xticColumn" type="data_column" data_ref="input" numerical="False" label="Use this column for X Tick labels" />
17        </when>
18        <when value="No">
19        </when>
20    </conditional>           
21    <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" />
22    <param name="title" type="text" size="30" value="Bar Chart" label="Plot title"/>
23    <param name="ylabel" type="text" size="30" value="V1" label="Label for Y axis"/>
24    <param name="ymin" type="integer" size="4" value="0" label="Minimal value on Y axis" help="set to 0 for autoscaling"/>
25    <param name="ymax" type="integer" size="4" value="0" label="Maximal value on Y axis" help="set to 0 for autoscaling"/>
26    <param name="pdf_size" type="select" label="Choose chart size (pixels)">
27        <option value="800,600">Normal: 800 by 600</option>
28        <option value="640,480">Small: 640 by 480</option>
29        <option value="1480,800">Large: 1480 by 800</option>
30        <option value="600,800">Normal Flipped: 600 by 800</option>
31        <option value="480,640">Small Flipped: 480 by 640</option>
32        <option value="800,1480">Large Flipped: 800 by 1480</option>
33    </param>
34  </inputs>
35  <outputs>
36    <data format="png" name="out_file1" />
37  </outputs>
38  <requirements>
39    <requirement type="python-module">Gnuplot</requirement>
40    <requirement type="python-module">Numeric</requirement>
41  </requirements>
42  <help>
43
44**What it does**
45
46This tool builds a bar chart on one or more columns. Suppose you have dataset like this one::
47
48  Gene1	10	15
49  Gene2	20	14
50  Gene3	67	45
51  Gene4	55	12
52
53Graphing columns 2 and 3 while using column 1 for X Tick Labels will produce the following plot:
54
55.. image:: ${static_path}/images/bar_chart.png 
56   :height: 324 
57   :width: 540 
58    
59</help>
60</tool>