Mercurial > repos > devteam > dna_filtering
annotate histogram2.xml @ 1:a60f7f660872 draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:17:35 -0400 |
| parents | 9c0d844f4e48 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="histogram_rpy" name="Histogram" version="1.0.3"> |
| 2 <description>of a numeric column</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.3">rpy</requirement> | |
| 5 <requirement type="package" version="2.11.0">R</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="python">histogram.py $input $out_file1 $numerical_column "$title" "$xlab" $breaks $density $frequency</command> | |
| 8 <inputs> | |
| 9 <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/> | |
| 10 <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" /> | |
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a60f7f660872
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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changeset
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11 <param name="breaks" type="integer" value="0" label="Number of breaks (bars)"/> |
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a60f7f660872
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
12 <param name="title" type="text" value="Histogram" label="Plot title"/> |
|
a60f7f660872
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
13 <param name="xlab" type="text" value="V1" label="Label for x axis"/> |
| 0 | 14 <param name="density" type="boolean" checked="yes" label="Include smoothed density"/> |
| 15 <param name="frequency" type="boolean" checked="no" label="Plot as frequency (counts)"/> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="pdf" name="out_file1" /> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="input" value="histogram_in1.tabular" ftype="tabular"/> | |
| 23 <param name="numerical_column" value="2"/> | |
| 24 <param name="breaks" value="0"/> | |
| 25 <param name="title" value="Histogram"/> | |
| 26 <param name="xlab" value="V1"/> | |
| 27 <param name="density" value="true"/> | |
| 28 <param name="frequency" value="false"/> | |
| 29 <output name="out_file1" file="histogram_out1.pdf"/> | |
| 30 </test> | |
| 31 </tests> | |
| 32 <help> | |
| 33 | |
| 34 .. class:: infomark | |
| 35 | |
| 36 **TIP:** To remove comment lines that do not begin with a *#* character, use *Text Manipulation->Remove beginning* | |
| 37 | |
| 38 .. class:: infomark | |
| 39 | |
| 40 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* | |
| 41 | |
| 42 ----- | |
| 43 | |
| 44 **Syntax** | |
| 45 | |
| 46 This tool computes a histogram of the numerical values in a column of a dataset. | |
| 47 | |
| 48 - All invalid, blank and comment lines in the dataset are skipped. The number of skipped lines is displayed in the resulting history item. | |
| 49 - **Column for x axis** - only numerical columns are possible. | |
| 50 - **Number of breaks(bars)** - breakpoints between histogram cells. Value of '0' will determine breaks automatically. | |
| 51 - **Plot title** - the histogram title. | |
| 52 - **Label for x axis** - the label of the x axis for the histogram. | |
| 53 - **Include smoothed density** - if checked, the resulting graph will join the given corresponding points with line segments. | |
| 54 | |
| 55 ----- | |
| 56 | |
| 57 **Example** | |
| 58 | |
| 59 - Input file:: | |
| 60 | |
| 61 1 68 4.1 | |
| 62 2 71 4.6 | |
| 63 3 62 3.8 | |
| 64 4 75 4.4 | |
| 65 5 58 3.2 | |
| 66 6 60 3.1 | |
| 67 7 67 3.8 | |
| 68 8 68 4.1 | |
| 69 9 71 4.3 | |
| 70 10 69 3.7 | |
| 71 | |
| 72 - Create a histogram on column 2 of the above dataset. | |
| 73 | |
| 74 .. image:: histogram2.png | |
| 75 | |
| 76 </help> | |
| 77 </tool> |