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/tools/plotting/scatterplot.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="scatterplot_rpy" name="Scatterplot">
 2  <description>of two numeric columns</description>
 3  <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command>
 4  <inputs>
 5    <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
 6    <param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
 7    <param name="col2" type="data_column" data_ref="input" numerical="True" label="Numerical column for y axis" />
 8    <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/>
 9    <param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/>
10    <param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/>
11  </inputs>
12  <outputs>
13    <data format="pdf" name="out_file1" />
14  </outputs>
15  <requirements>
16    <requirement type="python-module">rpy</requirement>
17  </requirements>
18  <!-- TODO: uncomment the following test when we have tools.update_state() working for 
19       multiple dependents with the same dependency.
20  <tests>
21    <test>
22      <param name="input" value="scatterplot_in1.tabular" ftype="tabular"/>
23      <param name="col1" value="2"/>
24      <param name="col2" value="3"/>
25      <param name="title" value="Scatterplot"/>
26      <param name="xlab" value="V1"/>
27      <param name="ylab" value="V2"/>
28      <output name="out_file1" file="scatterplot_out1.pdf" />
29    </test>
30  </tests>
31  -->
32  <help>
33
34.. class:: infomark
35
36**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
37
38-----
39
40**Syntax**
41
42This tool creates a simple scatter plot between two variables containing numeric values of a selected dataset. 
43
44- All invalid, blank and comment lines in the dataset are skipped.  The number of skipped lines is displayed in the resulting history item.
45
46- **Plot title** The scatterplot title
47- **Label for x axis** and **Label for y axis** The labels for x and y axis of the scatterplot.
48
49-----
50
51**Example**
52
53- Input file::
54
55    1   68  4.1
56    2   71  4.6
57    3   62  3.8
58    4   75  4.4
59    5   58  3.2
60    6   60  3.1
61    7   67  3.8
62    8   68  4.1
63    9   71  4.3
64    10  69  3.7 
65
66- Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset.
67
68.. image:: ${static_path}/images/scatterplot.png
69
70</help>
71</tool>