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scatterplot.xml
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100 lines (86 loc) · 3.4 KB
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<tool id="scatterplot_rpy" name="Scatterplot" version="1.0.3+galaxy0">
<description>of two numeric columns</description>
<requirements>
<requirement type="package" version="1.9">numpy</requirement>
<requirement type="package" version="2.8.5">rpy2</requirement>
<requirement type="package" version="3.0">libgfortran</requirement>
</requirements>
<!--
<environment_variables>
<environment_variable name="R_HOME">\$(R RHOME)</environment_variable>
</environment_variables> -->
<command><![CDATA[
python '$__tool_directory__/scatterplot.py'
'$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"/>
<conditional name="cols">
<param name="header" type="select" label="Does the table have a header?" refresh_on_change="true" help="If the table has a header, columns can be selected by name instead of the index.">
<option value="yes" selected="true">yes</option>
<option value="no">no</option>
</param>
<when value="yes">
<param name="col1" type="data_column" data_ref="input" use_header_names="true" numerical="True" label="Numerical column for x axis" />
<param name="col2" type="data_column" data_ref="input" use_header_names="true" numerical="True" label="Numerical column for y axis" />
</when>
<when value="no">
<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" />
</when>
</conditional>
<param name="title" type="text" value="Scatterplot" label="Plot title"/>
<param name="xlab" type="text" value="V1" label="Label for x axis"/>
<param name="ylab" type="text" value="V2" label="Label for y axis"/>
</inputs>
<outputs>
<data format="pdf" name="out_file1" />
</outputs>
<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" compare="sim_size" />
</test>
</tests>
<help><![CDATA[
.. 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:: scatterplot.png
]]>
</help>
<citations>
<citation type="doi">10.1038/s41586-020-2649-2</citation>
</citations>
</tool>