Mercurial > repos > devteam > dna_filtering
view histogram2.xml @ 1:a60f7f660872 draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author | devteam |
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date | Tue, 13 Oct 2015 12:17:35 -0400 |
parents | 9c0d844f4e48 |
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<tool id="histogram_rpy" name="Histogram" version="1.0.3"> <description>of a numeric column</description> <requirements> <requirement type="package" version="1.0.3">rpy</requirement> <requirement type="package" version="2.11.0">R</requirement> </requirements> <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" value="0" label="Number of breaks (bars)"/> <param name="title" type="text" value="Histogram" label="Plot title"/> <param name="xlab" type="text" 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" 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:: histogram2.png </help> </tool>