Mercurial > repos > nick > dna_visualizer
view 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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<tool id="visualdna" name="DNA visualizer" version="0.1"> <description>Visualize DNA with colored pixels.</description> <command interpreter="python">literal.py $input -o $output -c -s ${width}x${height} #if $colors.custom: -b $colors.background -G $colors.G -C $colors.C -A $colors.A -T $colors.T #end if </command> <inputs> <param name="input" type="data" format="fasta,text" label="Input sequence" /> <param name="width" type="integer" value="512" min="0" max="16384" label="Output image width" help="in pixels (max 16384)" /> <param name="height" type="integer" value="512" min="0" max="16384" label="Output image height" help="in pixels (max 16384)" /> <conditional name="colors"> <param name="custom" type="select" label="Base colors"> <option value="" selected="True">Use default colors</option> <option value="true">Use custom colors</option> </param> <when value=""> <!-- do nothing --> </when> <when value="true"> <!-- 'G':'255,255,255', 'C':'0,0,255', 'A':'0,255,0', 'T':'255,0,0' --> <param name="G" type="text" value="255,255,255" label="G RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> </param> <param name="C" type="text" value="0,0,255" label="C RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> </param> <param name="A" type="text" value="0,255,0" label="A RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> </param> <param name="T" type="text" value="255,0,0" label="T RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> </param> <param name="background" type="text" value="255,255,255" label="background RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> </param> </when> </conditional> </inputs> <outputs> <data name="output" format="png"/> </outputs> <help> .. class:: infomark **What it does** This tool convert DNA sequence into a PNG image by representing each base with one colored pixel. ----- .. class:: infomark **Input Format** 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. </help> </tool>