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1 <tool id="alignvis" name="heatmap">
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2 <description>of align output</description>
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3 <command interpreter="python"> alignvis.py $input $output $uselog $subset $reorder $color $scale </command>
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4 <inputs>
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5 <param name="input" format="tabular" type="data" label="Original file"/>
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6 <param name="uselog" label="log transform the data" type="boolean" truevalue="uselog" falsevalue="none" checked="True"/>
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7 <param name="subset" label="sample a subset if the data is too large" type="boolean" truevalue="subset" falsevalue="none" checked="True"/>
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8 <param name="scale" label="normalize by row/feature" type="boolean" truevalue="scale" falsevalue="none" checked="False"/>
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9 <param name="reorder" type="select" label="reorder features (rows)">
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10 <option value="none" selected="true">None</option>
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11 <option value="sort_by_sum">Sort row by sum</option>
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12 <option value="sort_by_center">Sort row by center </option>
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13 <option value="average">Cluster rows (average)</option>
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14 <option value="median">Cluster rows (median) </option>
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15 <option value="centroid">Cluster rows (centroid)</option>
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16 <option value="complete">Cluster rows (complete)</option>
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17 <option value="single">Cluster rows (single)</option>
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18 </param>
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19
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20 <param name="color" type="select" label="color scheme">
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21 <option value="heat" selected="true">heat</option>
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22 <option value="gray">gray</option>
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23 <option value="rainbow">rainbow</option>
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24 <option value="topo">topo</option>
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25 <option value="terrain">terrain</option>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data format="pdf" name="output" />
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30 </outputs>
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31 <help>
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32
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33 **What it does**
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34
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35 This tool generates a heatmap for output from 'align' tool. Each row is the color-coded coverage of a feature, and the features are sorted by the total coverage in the interval.
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36
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37 **Example**
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38
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39 .. image:: ./static/operation_icons/heatmap.png
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40
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41 </help>
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42 </tool>
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