/tools/plotting/scatterplot.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 71 lines · 43 code · 14 blank · 14 comment · 0 complexity · 9297a8f55a8b7eeac1830e3c75889e64 MD5 · raw file
- <tool id="scatterplot_rpy" name="Scatterplot">
- <description>of two numeric columns</description>
- <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command>
- <inputs>
- <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
- <param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
- <param name="col2" type="data_column" data_ref="input" numerical="True" label="Numerical column for y axis" />
- <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/>
- <param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/>
- <param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/>
- </inputs>
- <outputs>
- <data format="pdf" name="out_file1" />
- </outputs>
- <requirements>
- <requirement type="python-module">rpy</requirement>
- </requirements>
- <!-- TODO: uncomment the following test when we have tools.update_state() working for
- multiple dependents with the same dependency.
- <tests>
- <test>
- <param name="input" value="scatterplot_in1.tabular" ftype="tabular"/>
- <param name="col1" value="2"/>
- <param name="col2" value="3"/>
- <param name="title" value="Scatterplot"/>
- <param name="xlab" value="V1"/>
- <param name="ylab" value="V2"/>
- <output name="out_file1" file="scatterplot_out1.pdf" />
- </test>
- </tests>
- -->
- <help>
-
- .. class:: infomark
-
- **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
-
- -----
-
- **Syntax**
-
- This tool creates a simple scatter plot between two variables containing numeric values of a selected dataset.
-
- - All invalid, blank and comment lines in the dataset are skipped. The number of skipped lines is displayed in the resulting history item.
-
- - **Plot title** The scatterplot title
- - **Label for x axis** and **Label for y axis** The labels for x and y axis of the scatterplot.
-
- -----
-
- **Example**
-
- - Input file::
-
- 1 68 4.1
- 2 71 4.6
- 3 62 3.8
- 4 75 4.4
- 5 58 3.2
- 6 60 3.1
- 7 67 3.8
- 8 68 4.1
- 9 71 4.3
- 10 69 3.7
-
- - Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset.
-
- .. image:: ${static_path}/images/scatterplot.png
-
- </help>
- </tool>