Mercurial > repos > nick > dna_visualizer
annotate literal.xml @ 10:54223991334b default tip
tool_dependencies.xml: Defined PIL dependency
author | Nick Stoler <nstoler@psu.edu> |
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date | Mon, 03 Mar 2014 12:54:02 -0500 |
parents | 2d99feb4a8e3 |
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0 | 1 <tool id="visualdna" name="DNA visualizer" version="0.1"> |
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tool_dependencies.xml: Defined PIL dependency
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3 <requirements> |
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4 <requirement type="package" version="1.1.7">pil</requirement> |
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5 </requirements> |
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0 | 7 <description>Visualize DNA with colored pixels.</description> |
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9 <command interpreter="python">literal.py $input -o $output -c -s ${width}x${height} |
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10 #if $colors.custom: |
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11 -b $colors.background -G $colors.G -C $colors.C -A $colors.A -T $colors.T |
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12 #end if |
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13 </command> |
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0 | 15 <inputs> |
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16 <param name="input" type="data" format="fasta,text" label="Input sequence" /> |
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17 <param name="width" type="integer" value="512" min="0" max="16384" label="Output image width" help="in pixels (max 16384)" /> |
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18 <param name="height" type="integer" value="512" min="0" max="16384" label="Output image height" help="in pixels (max 16384)" /> |
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19 <conditional name="colors"> |
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20 <param name="custom" type="select" label="Base colors"> |
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21 <option value="" selected="True">Use default colors</option> |
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22 <option value="true">Use custom colors</option> |
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23 </param> |
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24 <when value=""> |
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25 <!-- do nothing --> |
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26 </when> |
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27 <when value="true"> |
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28 <!-- 'G':'255,255,255', 'C':'0,0,255', 'A':'0,255,0', 'T':'255,0,0' --> |
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29 <param name="background" type="text" value="255,255,255" label="Background RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> |
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30 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> |
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31 </param> |
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32 <param name="G" type="text" value="255,255,255" label="G RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> |
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33 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> |
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34 </param> |
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35 <param name="C" type="text" value="0,0,255" label="C RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> |
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36 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> |
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37 </param> |
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38 <param name="A" type="text" value="0,255,0" label="A RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> |
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39 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> |
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40 </param> |
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41 <param name="T" type="text" value="255,0,0" label="T RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> |
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42 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> |
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43 </param> |
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44 </when> |
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45 </conditional> |
0 | 46 </inputs> |
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47 |
0 | 48 <outputs> |
49 <data name="output" format="png"/> | |
50 </outputs> | |
51 | |
52 <help> | |
53 | |
54 .. class:: infomark | |
55 | |
56 **What it does** | |
57 | |
7 | 58 This tool converts DNA sequence into a PNG image by representing each base with one colored pixel. |
0 | 59 |
60 ----- | |
61 | |
62 .. class:: infomark | |
63 | |
64 **Input Format** | |
65 | |
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66 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. In a FASTA file with multiple sequences, all sequences will be used. |
0 | 67 |
68 </help> | |
69 | |
70 </tool> |