Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/TSS_distance.xml @ 0:cdd489d98766

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:50:41 -0400
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 <tool id="Annotation visualization" name="GIN visualizator" version="1.0.0">
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2 <description>of peaks distribution</description>
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3 <command interpreter="python">TSS_distance.py $input $out_file1 $numerical_column "$title" $window $breaks $density</command>
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4 <inputs>
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5 <param name="input" type="data" format="tabular" label="Dataset" help="Query missing? See TIP below"/>
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6 <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
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7 <param name="breaks" type="integer" size="4" value="20" label="Number of breaks (bars)"/>
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8 <param name="title" type="text" size="30" value="Histogram" label="Plot title"/>
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9 <param name="window" type="integer" size="10" value="4000" label="Zoom visualitazion"/>
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10 <param name="density" type="boolean" checked="yes" label="Include smoothed density"/>
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11 </inputs>
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12 <outputs>
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13 <data format="pdf" name="out_file1" />
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14 </outputs>
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15 <help>
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16
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17 .. class:: infomark
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18
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19 **What it does**
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20
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21 This tool generates a distribution of peaks with respect to their distance from TSS.
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22
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23 PLEASE, for more detailed information refer to the CARPET user Manual:
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24 click to download_ it.
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26 .. _download: /static/example_file/CARPET_userManual.zip
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28 -----
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30 .. class:: warningmark
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32 This tool requires at least 1 numerical column **"distance from TSS"**.
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34 -----
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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36 **Syntax**
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37
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38 - All invalid, blank and comment lines in the query are skipped. The number of skipped lines is displayed in the resulting history item.
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39 - **Numerical column for x axis** - only numerical columns are possible.
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40 - **Number of breaks(bars)** - breakpoints between histogram cells. Value of '0' will determine breaks automatically.
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41 - **Plot title** - the histogram title.
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42 - **Label for x axis** - the label of the x axis for the histogram.
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43 - **Zoom visualization** - Limit of the X axis. All the peaks falling beyond this limit are plotted in the last histogram cell.
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44 - **Include smoothed density** - if checked, the resulting graph will join the given corresponding points with line segments.
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46 -----
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47
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48 **Example**
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49
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50 - Input dataset ann_file from GIN (twelve columns: c1, c2, c3, c4, c5... c12):
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52 .. image:: static/images/CARPET/output_ann.png
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55 - Chose column **c12** ("Distance TSS").
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57 .. image:: static/images/CARPET/hist_ann.png
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59 </help>
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60 </tool>
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