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annotate scatterplot.xml @ 2:53eb2c412783 draft

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author devteam
date Fri, 18 Dec 2015 19:14:12 -0500
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1 <tool id="scatterplot_rpy" name="Scatterplot" version="1.0.1">
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2 <description>of two numeric columns</description>
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3 <requirements>
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4 <requirement type="package" version="1.9">numpy</requirement>
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5 <requirement type="package" version="1.0.3">rpy</requirement>
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6 </requirements>
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7 <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</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="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
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11 <param name="col2" type="data_column" data_ref="input" numerical="True" label="Numerical column for y axis" />
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12 <param name="title" type="text" value="Scatterplot" label="Plot title"/>
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13 <param name="xlab" type="text" value="V1" label="Label for x axis"/>
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14 <param name="ylab" type="text" value="V2" label="Label for y axis"/>
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15 </inputs>
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16 <outputs>
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17 <data format="pdf" name="out_file1" />
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18 </outputs>
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19 <!-- TODO: uncomment the following test when we have tools.update_state() working for
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20 multiple dependents with the same dependency.
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21 <tests>
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22 <test>
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23 <param name="input" value="scatterplot_in1.tabular" ftype="tabular"/>
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24 <param name="col1" value="2"/>
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25 <param name="col2" value="3"/>
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26 <param name="title" value="Scatterplot"/>
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27 <param name="xlab" value="V1"/>
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28 <param name="ylab" value="V2"/>
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29 <output name="out_file1" file="scatterplot_out1.pdf" />
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30 </test>
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31 </tests>
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32 -->
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33 <help>
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34 .. class:: infomark
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36 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
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38 -----
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40 **Syntax**
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42 This tool creates a simple scatter plot between two variables containing numeric values of a selected dataset.
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43
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44 - 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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45
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46 - **Plot title** The scatterplot title
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47 - **Label for x axis** and **Label for y axis** The labels for x and y axis of the scatterplot.
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49 -----
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51 **Example**
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53 - Input file::
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54
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55 1 68 4.1
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56 2 71 4.6
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57 3 62 3.8
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58 4 75 4.4
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59 5 58 3.2
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60 6 60 3.1
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61 7 67 3.8
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62 8 68 4.1
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63 9 71 4.3
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64 10 69 3.7
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65
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66 - Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset.
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67
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68 .. image:: scatterplot.png
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69 </help>
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70 </tool>