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