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comparison tools/plotting/bar_chart.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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
46 This 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
53 Graphing columns 2 and 3 while using column 1 for X Tick Labels will produce the following plot:
54
55 .. image:: ./static/images/bar_chart.png
56 :height: 324
57 :width: 540
58
59 </help>
60 </tool>