Mercurial > repos > nick > dna_visualizer
comparison literal.xml @ 5:58160195728e
Change color setting UI, allow background color setting, limit image size.
author | Nick Stoler <nstoler@psu.edu> |
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date | Sun, 02 Mar 2014 22:01:44 -0500 |
parents | 16772d7246e0 |
children | 0c552e103c93 |
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4:16772d7246e0 | 5:58160195728e |
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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 |