Mercurial > repos > xuebing > sharplabtool
diff mytools/plotmatrix.xml @ 7:f0dc65e7f6c0
Uploaded
author | xuebing |
---|---|
date | Fri, 09 Mar 2012 19:59:07 -0500 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mytools/plotmatrix.xml Fri Mar 09 19:59:07 2012 -0500 @@ -0,0 +1,43 @@ +<tool id="plotmatrix" name="matrix-visualization"> + <description>with sorting and clustering)</description> + <command interpreter="python"> plotmatrix.py $input $output $uselog $subset $reorder $color $scale $cols</command> + <inputs> + <param name="input" format="tabular" type="data" label="Data file"/> + <param name="cols" type="text" value="1,3,8:10" label="data columns" help="e.g.: column 1, 3, 8,9,10"/> + <param name="uselog" label="log transform the data" type="boolean" truevalue="uselog" falsevalue="none" checked="True"/> + <param name="subset" label="sample a subset if the data is too large" type="boolean" truevalue="subset" falsevalue="none" checked="True"/> + <param name="scale" label="normalize by row" type="boolean" truevalue="scale" falsevalue="none" checked="False"/> + <param name="reorder" type="select" label="reorder features (rows)"> + <option value="none" selected="true">None</option> + <option value="sort_by_sum">Sort row by sum</option> + <option value="sort_by_center">Sort row by center </option> + <option value="average">Cluster rows (average)</option> + <option value="median">Cluster rows (median) </option> + <option value="centroid">Cluster rows (centroid)</option> + <option value="complete">Cluster rows (complete)</option> + <option value="single">Cluster rows (single)</option> + </param> + + <param name="color" type="select" label="color scheme"> + <option value="heat" selected="true">heat</option> + <option value="gray">gray</option> + <option value="rainbow">rainbow</option> + <option value="topo">topo</option> + <option value="terrain">terrain</option> + </param> + </inputs> + <outputs> + <data format="pdf" name="output" /> + </outputs> + <help> + +**What it does** + +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. + +**Example** + +.. image:: ./static/operation_icons/heatmap.png + + </help> +</tool>