comparison histogram2.xml @ 0:9c0d844f4e48 draft

Imported from capsule None
author devteam
date Mon, 28 Jul 2014 11:30:12 -0400
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children a60f7f660872
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-1:000000000000 0:9c0d844f4e48
1 <tool id="histogram_rpy" name="Histogram" version="1.0.3">
2 <description>of a numeric column</description>
3 <requirements>
4 <requirement type="package" version="1.0.3">rpy</requirement>
5 <requirement type="package" version="2.11.0">R</requirement>
6 </requirements>
7 <command interpreter="python">histogram.py $input $out_file1 $numerical_column "$title" "$xlab" $breaks $density $frequency</command>
8 <inputs>
9 <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
10 <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
11 <param name="breaks" type="integer" size="4" value="0" label="Number of breaks (bars)"/>
12 <param name="title" type="text" size="30" value="Histogram" label="Plot title"/>
13 <param name="xlab" type="text" size="30" value="V1" label="Label for x axis"/>
14 <param name="density" type="boolean" checked="yes" label="Include smoothed density"/>
15 <param name="frequency" type="boolean" checked="no" label="Plot as frequency (counts)"/>
16 </inputs>
17 <outputs>
18 <data format="pdf" name="out_file1" />
19 </outputs>
20 <tests>
21 <test>
22 <param name="input" value="histogram_in1.tabular" ftype="tabular"/>
23 <param name="numerical_column" value="2"/>
24 <param name="breaks" value="0"/>
25 <param name="title" value="Histogram"/>
26 <param name="xlab" value="V1"/>
27 <param name="density" value="true"/>
28 <param name="frequency" value="false"/>
29 <output name="out_file1" file="histogram_out1.pdf"/>
30 </test>
31 </tests>
32 <help>
33
34 .. class:: infomark
35
36 **TIP:** To remove comment lines that do not begin with a *#* character, use *Text Manipulation-&gt;Remove beginning*
37
38 .. class:: infomark
39
40 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
41
42 -----
43
44 **Syntax**
45
46 This tool computes a histogram of the numerical values in a column of a dataset.
47
48 - All invalid, blank and comment lines in the dataset are skipped. The number of skipped lines is displayed in the resulting history item.
49 - **Column for x axis** - only numerical columns are possible.
50 - **Number of breaks(bars)** - breakpoints between histogram cells. Value of '0' will determine breaks automatically.
51 - **Plot title** - the histogram title.
52 - **Label for x axis** - the label of the x axis for the histogram.
53 - **Include smoothed density** - if checked, the resulting graph will join the given corresponding points with line segments.
54
55 -----
56
57 **Example**
58
59 - Input file::
60
61 1 68 4.1
62 2 71 4.6
63 3 62 3.8
64 4 75 4.4
65 5 58 3.2
66 6 60 3.1
67 7 67 3.8
68 8 68 4.1
69 9 71 4.3
70 10 69 3.7
71
72 - Create a histogram on column 2 of the above dataset.
73
74 .. image:: histogram2.png
75
76 </help>
77 </tool>