Mercurial > repos > devteam > scatterplot
diff scatterplot.xml @ 2:4f8b9e70fda0 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 93df3895fbf2fa44ff279303093fb89b79081687
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2016 11:14:37 -0400 |
| parents | d243056b22ed |
| children | efda9a4a50e7 |
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--- a/scatterplot.xml Fri Oct 09 17:17:55 2015 -0400 +++ b/scatterplot.xml Thu Sep 15 11:14:37 2016 -0400 @@ -1,71 +1,69 @@ -<tool id="scatterplot_rpy" name="Scatterplot" version="1.0.0"> - <description>of two numeric columns</description> - <requirements> - <requirement type="package" version="1.0.3">rpy</requirement> - </requirements> - <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" 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> - <!-- 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:: scatterplot.png - -</help> -</tool> +<tool id="scatterplot_rpy" name="Scatterplot" version="1.0.2"> + <description>of two numeric columns</description> + <requirements> + <requirement type="package" version="1.9">numpy</requirement> + <!-- explicit R requirement is necessary for toolshed package, conda rpy2 comes with R --> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="2.7.8">rpy2</requirement> + </requirements> + <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" 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> +.. 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> +</tool>