Mercurial > repos > mvdbeek > scatterplot_test
annotate scatterplot.xml @ 1:b4102b163488 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
| author | mvdbeek |
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| date | Wed, 14 Sep 2016 12:42:56 -0400 |
| parents | 11627baf830e |
| children | ca89930cb23c |
| rev | line source |
|---|---|
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b4102b163488
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
mvdbeek
parents:
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1 <tool id="scatterplot_rpy" name="Scatterplot" version="1.0.2"> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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2 <description>of two numeric columns</description> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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3 <requirements> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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4 <requirement type="package" version="1.9">numpy</requirement> |
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b4102b163488
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
mvdbeek
parents:
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5 <requirement type="package" version="2.7.8">rpy2</requirement> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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changeset
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6 </requirements> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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7 <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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changeset
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8 <inputs> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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9 <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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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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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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changeset
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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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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
changeset
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12 <param name="title" type="text" value="Scatterplot" label="Plot title"/> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
changeset
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13 <param name="xlab" type="text" value="V1" label="Label for x axis"/> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
changeset
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14 <param name="ylab" type="text" value="V2" label="Label for y axis"/> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
changeset
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15 </inputs> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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16 <outputs> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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17 <data format="pdf" name="out_file1" /> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
changeset
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18 </outputs> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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19 <tests> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
changeset
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20 <test> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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changeset
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21 <param name="input" value="scatterplot_in1.tabular" ftype="tabular"/> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
changeset
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22 <param name="col1" value="2"/> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
changeset
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23 <param name="col2" value="3"/> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
changeset
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24 <param name="title" value="Scatterplot"/> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
changeset
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25 <param name="xlab" value="V1"/> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
changeset
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26 <param name="ylab" value="V2"/> |
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1
b4102b163488
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 1b68ca3d083c5879e996a9df5e22963dfc9c3f90-dirty
mvdbeek
parents:
0
diff
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27 <output name="out_file1" file="scatterplot_out1.pdf" compare="sim_size" /> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
changeset
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28 </test> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
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29 </tests> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
diff
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30 <help> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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31 .. class:: infomark |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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32 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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33 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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34 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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35 ----- |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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36 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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37 **Syntax** |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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38 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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39 This tool creates a simple scatter plot between two variables containing numeric values of a selected dataset. |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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40 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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41 - 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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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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42 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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43 - **Plot title** The scatterplot title |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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44 - **Label for x axis** and **Label for y axis** The labels for x and y axis of the scatterplot. |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
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45 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
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46 ----- |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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47 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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48 **Example** |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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49 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
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50 - Input file:: |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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51 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
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52 1 68 4.1 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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53 2 71 4.6 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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54 3 62 3.8 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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55 4 75 4.4 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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56 5 58 3.2 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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57 6 60 3.1 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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58 7 67 3.8 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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59 8 68 4.1 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
parents:
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60 9 71 4.3 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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61 10 69 3.7 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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62 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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63 - Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset. |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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64 |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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65 .. image:: scatterplot.png |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
mvdbeek
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66 </help> |
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11627baf830e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
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67 </tool> |