mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Ramkrishna Chakrabarty
1bac740073
- now the tool requires the user to enter the specific columns indicating ref base, position, and start of a sample - added an interactive zoom option. when this option is selected, the image can be zoomed in or out using the mouse wheel. - fixed the firefox & opera problems in displaying the svg image
61 lines
2.2 KiB
XML
61 lines
2.2 KiB
XML
<tool id="mutation_visualize" name="Mutation Visualization" version="1.0.0">
|
|
<description></description>
|
|
<command interpreter="python">
|
|
visualize.py
|
|
--input-file=$input1
|
|
--output-file=$out_file1
|
|
--zoom=$zoom_value
|
|
--position_col=$position_col
|
|
--ref_col=$ref_col
|
|
#for $f in $sample_chooser:
|
|
"${f.name}"
|
|
${f.a_col}
|
|
${f.totals_col}
|
|
#end for
|
|
</command>
|
|
<inputs>
|
|
<param format="tabular" name="input1" type="data" label="Compare sequences in"></param>
|
|
<param name="position_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Position Column" help="" />
|
|
<param name="ref_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Reference Base Column" help="" />
|
|
|
|
<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="totals_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Totals Column" help="" />
|
|
</repeat>
|
|
|
|
<param name="zoom_value" type="select" label="Zoom">
|
|
<option value="1">1x</option>
|
|
<option value="2">2x</option>
|
|
<option value="3">3x</option>
|
|
<option value="4">4x</option>
|
|
<option value="5">5x</option>
|
|
<option value="interactive">Interactive</option>
|
|
</param>
|
|
|
|
</inputs>
|
|
<outputs>
|
|
<data format="svg" name="out_file1" />
|
|
</outputs>
|
|
<help>
|
|
|
|
**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
|
|
|
|
Visualization:
|
|
|
|
.. image:: ../static/images/mutation_visualization_example.png
|
|
:width: 150
|
|
|
|
Interactivity::
|
|
If interactive zoom/pan option is checked then the resultant image can be zoomed in or out: scroll mouse wheel; pan: drag using left mouse button.
|
|
|
|
</help>
|
|
</tool>
|