Mercurial > repos > matces > carpet_toolsuite
view carpet-src-1/tools/CARPET/TSS_distance.xml @ 1:78770028dcf1 default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | matces |
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date | Tue, 07 Jun 2011 16:59:33 -0400 |
parents | cdd489d98766 |
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<tool id="Annotation visualization" name="GIN visualizator" version="1.0.0"> <description>of peaks distribution</description> <command interpreter="python">TSS_distance.py $input $out_file1 $numerical_column "$title" $window $breaks $density</command> <inputs> <param name="input" type="data" format="tabular" label="Dataset" help="Query missing? See TIP below"/> <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" /> <param name="breaks" type="integer" size="4" value="20" label="Number of breaks (bars)"/> <param name="title" type="text" size="30" value="Histogram" label="Plot title"/> <param name="window" type="integer" size="10" value="4000" label="Zoom visualitazion"/> <param name="density" type="boolean" checked="yes" label="Include smoothed density"/> </inputs> <outputs> <data format="pdf" name="out_file1" /> </outputs> <help> .. class:: infomark **What it does** This tool generates a distribution of peaks with respect to their distance from TSS. PLEASE, for more detailed information refer to the CARPET user Manual: click to download_ it. .. _download: /static/example_file/CARPET_userManual.zip ----- .. class:: warningmark This tool requires at least 1 numerical column **"distance from TSS"**. ----- **Syntax** - All invalid, blank and comment lines in the query are skipped. The number of skipped lines is displayed in the resulting history item. - **Numerical column for x axis** - only numerical columns are possible. - **Number of breaks(bars)** - breakpoints between histogram cells. Value of '0' will determine breaks automatically. - **Plot title** - the histogram title. - **Label for x axis** - the label of the x axis for the histogram. - **Zoom visualization** - Limit of the X axis. All the peaks falling beyond this limit are plotted in the last histogram cell. - **Include smoothed density** - if checked, the resulting graph will join the given corresponding points with line segments. ----- **Example** - Input dataset ann_file from GIN (twelve columns: c1, c2, c3, c4, c5... c12): .. image:: static/images/CARPET/output_ann.png - Chose column **c12** ("Distance TSS"). .. image:: static/images/CARPET/hist_ann.png </help> </tool>