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comparison literal.xml @ 5:58160195728e

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Change color setting UI, allow background color setting, limit image size.
author Nick Stoler <nstoler@psu.edu>
date Sun, 02 Mar 2014 22:01:44 -0500
parents 16772d7246e0
children 0c552e103c93
comparison
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4:16772d7246e0 5:58160195728e
1 <tool id="visualdna" name="DNA visualizer" version="0.1"> 1 <tool id="visualdna" name="DNA visualizer" version="0.1">
2 <description>Visualize DNA with colored pixels.</description> 2 <description>Visualize DNA with colored pixels.</description>
3 <command interpreter="python">literal.py $input -o $output -c -s ${width}x${height} 3 <command interpreter="python">literal.py $input -o $output -c -s ${width}x${height}
4 #if $colors.custom: 4 #if $colors.custom:
5 -A $colors.AR,$colors.AG,$colors.AB -T $colors.TR,$colors.TG,$colors.TB -G $colors.GR,$colors.GG,$colors.GB -C $colors.CR,$colors.CG,$colors.CB 5 -b $colors.background -G $colors.G -C $colors.C -A $colors.A -T $colors.T
6 #end if 6 #end if
7 </command> 7 </command>
8 <inputs> 8 <inputs>
9 <param name="input" type="data" format="fasta,text" label="Input sequence" /> 9 <param name="input" type="data" format="fasta,text" label="Input sequence" />
10 <param name="width" type="integer" value="512" label="Output image width" help="in pixels" /> 10 <param name="width" type="integer" value="512" min="0" max="16384" label="Output image width" help="in pixels (max 16384)" />
11 <param name="height" type="integer" value="512" label="Output image height" help="in pixels" /> 11 <param name="height" type="integer" value="512" min="0" max="16384" label="Output image height" help="in pixels (max 16384)" />
12 <conditional name="colors"> 12 <conditional name="colors">
13 <param name="custom" type="select" label="Base colors"> 13 <param name="custom" type="select" label="Base colors">
14 <option value="" selected="True">Use default colors</option> 14 <option value="" selected="True">Use default colors</option>
15 <option value="true">Use custom colors</option> 15 <option value="true">Use custom colors</option>
16 </param> 16 </param>
17 <when value=""> 17 <when value="">
18 <!-- do nothing --> 18 <!-- do nothing -->
19 </when> 19 </when>
20 <when value="true"> 20 <when value="true">
21 <!-- 'A':'0,255,0', 'T':'255,0,0', 'G':'255,255,255', 'C':'0,0,255' --> 21 <!-- 'G':'255,255,255', 'C':'0,0,255', 'A':'0,255,0', 'T':'255,0,0' -->
22 <param name="AR" type="integer" value="0" label="A red value" /> 22 <param name="G" type="text" value="255,255,255" label="G RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)">
23 <param name="AG" type="integer" value="255" label="A green value" /> 23 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator>
24 <param name="AB" type="integer" value="0" label="A blue value" /> 24 </param>
25 <param name="TR" type="integer" value="255" label="T red value" /> 25 <param name="C" type="text" value="0,0,255" label="C RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)">
26 <param name="TG" type="integer" value="0" label="T green value" /> 26 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator>
27 <param name="TB" type="integer" value="0" label="T blue value" /> 27 </param>
28 <param name="GR" type="integer" value="255" label="G red value" /> 28 <param name="A" type="text" value="0,255,0" label="A RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)">
29 <param name="GG" type="integer" value="255" label="G green value" /> 29 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator>
30 <param name="GB" type="integer" value="255" label="G blue value" /> 30 </param>
31 <param name="CR" type="integer" value="0" label="C red value" /> 31 <param name="T" type="text" value="255,0,0" label="T RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)">
32 <param name="CG" type="integer" value="0" label="C green value" /> 32 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator>
33 <param name="CB" type="integer" value="255" label="C blue value" /> 33 </param>
34 <param name="background" type="text" value="255,255,255" label="background RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)">
35 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator>
36 </param>
34 </when> 37 </when>
35 </conditional> 38 </conditional>
36 </inputs> 39 </inputs>
37 <outputs> 40 <outputs>
38 <data name="output" format="png"/> 41 <data name="output" format="png"/>
39 </outputs> 42 </outputs>
40 <stdio>
41 <exit_code range="1:" err_level="fatal"/>
42 <exit_code range=":-1" err_level="fatal"/>
43 </stdio>
44 43
45 <help> 44 <help>
46 45
47 .. class:: infomark 46 .. class:: infomark
48 47