Mercurial > repos > nick > dna_visualizer
view literal.xml @ 4:16772d7246e0
literal.xml: need to clobber output file
author | Nick Stoler <nstoler@psu.edu> |
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date | Sun, 02 Mar 2014 15:02:00 -0500 |
parents | 3c5c4e3cccab |
children | 58160195728e |
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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: -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 #end if </command> <inputs> <param name="input" type="data" format="fasta,text" label="Input sequence" /> <param name="width" type="integer" value="512" label="Output image width" help="in pixels" /> <param name="height" type="integer" value="512" label="Output image height" help="in pixels" /> <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"> <!-- 'A':'0,255,0', 'T':'255,0,0', 'G':'255,255,255', 'C':'0,0,255' --> <param name="AR" type="integer" value="0" label="A red value" /> <param name="AG" type="integer" value="255" label="A green value" /> <param name="AB" type="integer" value="0" label="A blue value" /> <param name="TR" type="integer" value="255" label="T red value" /> <param name="TG" type="integer" value="0" label="T green value" /> <param name="TB" type="integer" value="0" label="T blue value" /> <param name="GR" type="integer" value="255" label="G red value" /> <param name="GG" type="integer" value="255" label="G green value" /> <param name="GB" type="integer" value="255" label="G blue value" /> <param name="CR" type="integer" value="0" label="C red value" /> <param name="CG" type="integer" value="0" label="C green value" /> <param name="CB" type="integer" value="255" label="C blue value" /> </when> </conditional> </inputs> <outputs> <data name="output" format="png"/> </outputs> <stdio> <exit_code range="1:" err_level="fatal"/> <exit_code range=":-1" err_level="fatal"/> </stdio> <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>