Mercurial > repos > nick > dna_visualizer
comparison literal.xml @ 1:717a4009675c
literal.xml: adding custom color support
author | Nick Stoler <nstoler@psu.edu> |
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date | Sun, 02 Mar 2014 14:20:33 -0500 |
parents | 5257ce9d9184 |
children | 1695b2153760 |
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0:5257ce9d9184 | 1:717a4009675c |
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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 -s ${width}x${height} </command> | 3 <command interpreter="python">literal.py $input -o $output -s ${width}x${height} |
4 #if $colors.custom: | |
5 -A $AR,$AG,$AB -T $TR,$TG,$TB -G $GR,$GG,$GB -C $CR,$CG,$CB | |
6 #end if | |
7 </command> | |
4 <inputs> | 8 <inputs> |
5 <param name="input" type="data" format="fasta" label="Input sequence" /> | 9 <param name="input" type="data" format="fasta" label="Input sequence" /> |
6 <param name="width" type="integer" value="512" min="512" label="Output image width" help="in pixels" /> | 10 <param name="width" type="integer" value="512" min="512" label="Output image width" help="in pixels" /> |
7 <param name="height" type="integer" value="512" min="512" label="Output image height" help="in pixels" /> | 11 <param name="height" type="integer" value="512" min="512" label="Output image height" help="in pixels" /> |
12 <conditional name="colors"> | |
13 <param name="custom" type="select" label="Base colors"> | |
14 <option value="" selected="True">Use default colors</option> | |
15 <option value="true">Use custom colors</option> | |
16 </param> | |
17 <when value=""> | |
18 <!-- do nothing --> | |
19 </when> | |
20 <when value="true"> | |
21 <!-- 'A':'0,255,0', 'T':'255,0,0', 'G':'255,255,255', 'C':'0,0,255' --> | |
22 <param name="AR" type="integer" value="0" label="A red value" /> | |
23 <param name="AG" type="integer" value="255" label="A green value" /> | |
24 <param name="AB" type="integer" value="0" label="A blue value" /> | |
25 <param name="TR" type="integer" value="255" label="T red value" /> | |
26 <param name="TG" type="integer" value="0" label="T green value" /> | |
27 <param name="TB" type="integer" value="0" label="T blue value" /> | |
28 <param name="GR" type="integer" value="255" label="G red value" /> | |
29 <param name="GG" type="integer" value="255" label="G green value" /> | |
30 <param name="GB" type="integer" value="255" label="G blue value" /> | |
31 <param name="CR" type="integer" value="0" label="C red value" /> | |
32 <param name="CG" type="integer" value="0" label="C green value" /> | |
33 <param name="CB" type="integer" value="255" label="C blue value" /> | |
34 </when> | |
35 </conditional> | |
8 </inputs> | 36 </inputs> |
9 <outputs> | 37 <outputs> |
10 <data name="output" format="png"/> | 38 <data name="output" format="png"/> |
11 </outputs> | 39 </outputs> |
12 <stdio> | 40 <stdio> |