Mercurial > repos > nick > dna_visualizer
annotate 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 |
rev | line source |
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0 | 1 <tool id="visualdna" name="DNA visualizer" version="0.1"> |
2 <description>Visualize DNA with colored pixels.</description> | |
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literal.xml: adding custom color support
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3 <command interpreter="python">literal.py $input -o $output -s ${width}x${height} |
717a4009675c
literal.xml: adding custom color support
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4 #if $colors.custom: |
717a4009675c
literal.xml: adding custom color support
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5 -A $AR,$AG,$AB -T $TR,$TG,$TB -G $GR,$GG,$GB -C $CR,$CG,$CB |
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6 #end if |
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7 </command> |
0 | 8 <inputs> |
9 <param name="input" type="data" format="fasta" label="Input sequence" /> | |
10 <param name="width" type="integer" value="512" min="512" label="Output image width" help="in pixels" /> | |
11 <param name="height" type="integer" value="512" min="512" label="Output image height" help="in pixels" /> | |
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literal.xml: adding custom color support
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12 <conditional name="colors"> |
717a4009675c
literal.xml: adding custom color support
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13 <param name="custom" type="select" label="Base colors"> |
717a4009675c
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14 <option value="" selected="True">Use default colors</option> |
717a4009675c
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Nick Stoler <nstoler@psu.edu>
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15 <option value="true">Use custom colors</option> |
717a4009675c
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Nick Stoler <nstoler@psu.edu>
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16 </param> |
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17 <when value=""> |
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18 <!-- do nothing --> |
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19 </when> |
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20 <when value="true"> |
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21 <!-- 'A':'0,255,0', 'T':'255,0,0', 'G':'255,255,255', 'C':'0,0,255' --> |
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22 <param name="AR" type="integer" value="0" label="A red value" /> |
717a4009675c
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23 <param name="AG" type="integer" value="255" label="A green value" /> |
717a4009675c
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24 <param name="AB" type="integer" value="0" label="A blue value" /> |
717a4009675c
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25 <param name="TR" type="integer" value="255" label="T red value" /> |
717a4009675c
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26 <param name="TG" type="integer" value="0" label="T green value" /> |
717a4009675c
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27 <param name="TB" type="integer" value="0" label="T blue value" /> |
717a4009675c
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28 <param name="GR" type="integer" value="255" label="G red value" /> |
717a4009675c
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29 <param name="GG" type="integer" value="255" label="G green value" /> |
717a4009675c
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30 <param name="GB" type="integer" value="255" label="G blue value" /> |
717a4009675c
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31 <param name="CR" type="integer" value="0" label="C red value" /> |
717a4009675c
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32 <param name="CG" type="integer" value="0" label="C green value" /> |
717a4009675c
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33 <param name="CB" type="integer" value="255" label="C blue value" /> |
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34 </when> |
717a4009675c
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35 </conditional> |
0 | 36 </inputs> |
37 <outputs> | |
38 <data name="output" format="png"/> | |
39 </outputs> | |
40 <stdio> | |
41 <exit_code range="1:" err_level="fatal"/> | |
42 <exit_code range=":-1" err_level="fatal"/> | |
43 </stdio> | |
44 | |
45 <help> | |
46 | |
47 .. class:: infomark | |
48 | |
49 **What it does** | |
50 | |
51 This tool convert DNA sequence into a PNG image by representing each base with one colored pixel. | |
52 | |
53 ----- | |
54 | |
55 .. class:: infomark | |
56 | |
57 **Input Format** | |
58 | |
59 The input sequence can be in FASTA format or a plain text file containing only the sequence. Any non-ATGC characters (case-insensitive) will be skipped. | |
60 | |
61 </help> | |
62 | |
63 </tool> |