# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287520820 14400 # Node ID ad9bb65d2d153af5db0ae497930eb35d17f63057 # Parent 35b379691524c768ec84f86477f1ab49859afec2 mutation viz tool help cleanup --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -20,7 +20,7 @@ <repeat name="sample_chooser" title="Sample"><param name="name" type="text" label="Label" help="Optional" /> - <param name="a_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="A Column" help="" /> + <param name="a_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Base A Column" help="" /><param name="totals_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Totals Column" help="" /></repeat> @@ -60,27 +60,42 @@ </test></tests><help> - -**Example** +**What it does** This tool allows you to visualize mutations described in a tabular input file. It generates an SVG image which can be viewed in any web browser. +You will need to specify the position and reference columns in the input file. Then click on the 'Add new Sample' to add samples in the input file that you would like to visualize. For each sample you select, specify the column for base 'A', the totals column and enter a name. +This tool assumes the columns specifying bases A, C, G, T are placed consecutively and in that order in an input file. + +Interactivity: If interactive zoom option is selected, then the resultant image can be zoomed in or out using the scroll mouse wheel and can be panned by dragging the image using left mouse button. + +----- + +**General Example** + Given the input file:: - gm blood gm cheek chrM 72 73 G 26394 4 49 0 26447 26398 1 23389 3 45 0 23437 23392 1 chrM 149 150 T 11 50422 2 96 50531 50435 1 4 45417 1 65 45487 45422 1 -You will need to specify the position and reference columns in the input file. Then click on the 'Add new Sample' to add samples in the input file that you would like to visualize. For each sample you select, specify the column for base 'A' and the totals column. -This tool assumes the columns specifying bases A, C, G, T are placed consecutively and in that order in an input file. +To visualize the two samples in the input file, the following parameters are selected before running the tool:: + + Position column: 2 + Reference Base column: 4 + Sample 1 Label: gm blood + Sample 1 Base A column: 5 + Sample 1 Totals column: 9 + Sample 2 Label: gm cheek + Sample 2 Base A column: 12 + Sample 2 Totals column: 16 -Visualization: +Visualization output: .. image:: ../static/images/mutation_visualization_example.png :width: 150 -Interactivity:: - If interactive zoom option is selected, then the resultant image can be zoomed in or out using the scroll mouse wheel and can be panned by dragging the image using left mouse button. +Here the left-most column represents the position and the background color is the reference base color. Each column on its right describe each sample. +In the output above, the blue bar is the longest, which means that base A is maximum in position 72 for both the samples. </help></tool>