Mercurial > repos > iuc > rpy_statistics_collection
diff histogram.xml @ 1:2e7bc1bb2dbe draft default tip
Uploaded
| author | iuc |
|---|---|
| date | Fri, 09 Jan 2015 12:56:07 -0500 |
| parents | ffcdde989859 |
| children |
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--- a/histogram.xml Tue Jul 29 06:30:45 2014 -0400 +++ b/histogram.xml Fri Jan 09 12:56:07 2015 -0500 @@ -1,77 +1,91 @@ -<tool id="histogram_rpy" name="Histogram" version="1.1.0"> - <description>of a numeric column</description> - <expand macro="requirements" /> - <macros> - <import>statistic_tools_macros.xml</import> - </macros> - <command interpreter="python">histogram.py $input $out_file1 $numerical_column "$title" "$xlab" $breaks $density $frequency</command> - <inputs> - <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/> - <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" /> - <param name="breaks" type="integer" size="4" value="0" label="Number of breaks (bars)"/> - <param name="title" type="text" size="30" value="Histogram" label="Plot title"/> - <param name="xlab" type="text" size="30" value="V1" label="Label for x axis"/> - <param name="density" type="boolean" checked="yes" label="Include smoothed density"/> - <param name="frequency" type="boolean" checked="no" label="Plot as frequency (counts)"/> - </inputs> - <outputs> - <data format="pdf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="input" value="histogram_in1.tabular" ftype="tabular"/> - <param name="numerical_column" value="2"/> - <param name="breaks" value="0"/> - <param name="title" value="Histogram"/> - <param name="xlab" value="V1"/> - <param name="density" value="true"/> - <param name="frequency" value="false"/> - <output name="out_file1" lines_diff="10" file="histogram_out1.pdf"/> - </test> - </tests> - <help> - -.. class:: infomark - -**TIP:** To remove comment lines that do not begin with a *#* character, use *Text Manipulation->Remove beginning* - - .. class:: infomark - -**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* - ------ - -**Syntax** - -This tool computes a histogram of the numerical values in a column of a dataset. - -- All invalid, blank and comment lines in the dataset are skipped. The number of skipped lines is displayed in the resulting history item. -- **Column for x axis** - only numerical columns are possible. -- **Number of breaks(bars)** - breakpoints between histogram cells. Value of '0' will determine breaks automatically. -- **Plot title** - the histogram title. -- **Label for x axis** - the label of the x axis for the histogram. -- **Include smoothed density** - if checked, the resulting graph will join the given corresponding points with line segments. - ------ - -**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 histogram on column 2 of the above dataset. - -.. image:: $PATH_TO_IMAGES/histogram2.png - -</help> -</tool> +<tool id="histogram_rpy" name="Histogram" version="1.1.0"> + <description>of a numeric column</description> + <expand macro="requirements" /> + <macros> + <import>statistic_tools_macros.xml</import> + </macros> + <command interpreter="python"> +<![CDATA[ + histogram.py + $input + $out_file1 + $numerical_column + "$title" + "$xlab" + $breaks + $density + $frequency +]]> + </command> + <inputs> + <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/> + <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" /> + <param name="breaks" type="integer" size="4" value="0" label="Number of breaks (bars)"/> + <param name="title" type="text" size="30" value="Histogram" label="Plot title"/> + <param name="xlab" type="text" size="30" value="V1" label="Label for x axis"/> + <param name="density" type="boolean" checked="yes" label="Include smoothed density"/> + <param name="frequency" type="boolean" checked="no" label="Plot as frequency (counts)"/> + </inputs> + <outputs> + <data format="pdf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input" value="histogram_in1.tabular" ftype="tabular"/> + <param name="numerical_column" value="2"/> + <param name="breaks" value="0"/> + <param name="title" value="Histogram"/> + <param name="xlab" value="V1"/> + <param name="density" value="true"/> + <param name="frequency" value="false"/> + <output name="out_file1" lines_diff="10" file="histogram_out1.pdf"/> + </test> + </tests> + <help> +<![CDATA[ + +.. class:: infomark + +**TIP:** To remove comment lines that do not begin with a *#* character, use *Text Manipulation->Remove beginning* + + .. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* + +----- + +**Syntax** + +This tool computes a histogram of the numerical values in a column of a dataset. + +- All invalid, blank and comment lines in the dataset are skipped. The number of skipped lines is displayed in the resulting history item. +- **Column for x axis** - only numerical columns are possible. +- **Number of breaks(bars)** - breakpoints between histogram cells. Value of '0' will determine breaks automatically. +- **Plot title** - the histogram title. +- **Label for x axis** - the label of the x axis for the histogram. +- **Include smoothed density** - if checked, the resulting graph will join the given corresponding points with line segments. + +----- + +**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 histogram on column 2 of the above dataset. + +.. image:: $PATH_TO_IMAGES/histogram2.png + +]]> + </help> +</tool>