root/galaxy-central/tools/plotting/histogram2.xml

リビジョン 2, 2.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="histogram_rpy" name="Histogram" version="1.0.2">
2  <description>of a numeric column</description>
3  <command interpreter="python">histogram.py $input $out_file1 $numerical_column "$title" "$xlab" $breaks $density</command>
4  <inputs>
5    <param name="input" type="data" format="tabular" label="Dataset" help="Query missing? See TIP below"/>
6    <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
7    <param name="breaks" type="integer" size="4" value="0" label="Number of breaks (bars)"/>
8    <param name="title" type="text" size="30" value="Histogram" label="Plot title"/>
9    <param name="xlab" type="text" size="30" value="V1" label="Label for x axis"/>
10    <param name="density" type="boolean" checked="yes" label="Include smoothed density"/>
11  </inputs>
12  <outputs>
13    <data format="pdf" name="out_file1" />
14  </outputs>
15  <tests>
16    <test>
17      <param name="input" value="histogram_in1.tabular" ftype="tabular"/>
18      <param name="numerical_column" value="2"/>
19      <param name="breaks" value="0"/>
20      <param name="title" value="Histogram"/>
21      <param name="xlab" value="V1"/>
22      <param name="density" value="true"/>
23      <output name="out_file1" file="histogram_out1.pdf" />
24    </test>
25  </tests>
26  <requirements>
27    <requirement type="python-module">rpy</requirement>
28  </requirements>
29  <help>
30
31.. class:: infomark
32
33**TIP:** To remove comment lines that do not begin with a *#* character, use *Text Manipulation-&gt;Remove beginning*
34
35 .. class:: infomark
36
37**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
38
39-----
40
41**Syntax**
42
43This tool computes a histogram of the numerical values in a column of a query.
44
45- All invalid, blank and comment lines in the query are skipped.  The number of skipped lines is displayed in the resulting history item.
46- **Column for x axis** - only numerical columns are possible.
47- **Number of breaks(bars)** - breakpoints between histogram cells. Value of '0' will determine breaks automatically.
48- **Plot title** - the histogram title.
49- **Label for x axis** - the label of the x axis for the histogram.
50- **Include smoothed density** - if checked, the resulting graph will join the given corresponding points with line segments.
51
52-----
53
54**Example**
55
56- Input file::
57
58    1   68      4.1
59    2   71      4.6
60    3   62      3.8
61    4   75      4.4
62    5   58      3.2
63    6   60      3.1
64    7   67      3.8
65    8   68      4.1
66    9   71      4.3
67    10  69      3.7
68
69- Create a histogram on column 2 of the above dataset.
70
71.. image:: ../static/images/histogram2.png
72
73</help>
74</tool>
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