comparison bigwig_to_wig.xml @ 0:99dc4bdb1d35 draft

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author nikos
date Tue, 05 Aug 2014 07:44:03 -0400
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1 <tool id="bigwig_to_wig" name="BigWig to Wig" version="1.0.2">
2 <description>converter</description>
3 <command>bigwig_to_wig.sh -f $input -b $bin_size -l $mylab > $output </command>
4 <requirements>
5 <requirement type="package">bigWigSummary</requirement>
6 <requirement type="package">bigWigInfo</requirement>
7 </requirements>
8 <inputs>
9 <param format="bigwig" name="input" type="data" label="BigWig file to convert" />
10 <param name="bin_size" size="4" type="integer" value="500" label="Bin size" help="Must be an even integer > 100." />
11 <param name="mylab" type="text" value="wiggle_file" label="Output file prefix" help="" />
12 </inputs>
13 <outputs>
14 <data format="wig" name="output" label="${mylab}_density_bin${bin_size}.wig" />
15 </outputs>
16 <tests>
17 <test>
18 <param name="input" value="1.bigwig" />
19 <param name="bin_size" value="500" />
20 <output name="output" file="1.wig" />
21 <test>
22 </tests>
23 <help>
24
25 This tool converts a **BigWig** file to fixed step **Wiggle** format.
26 Resolution is controlled through the bin size (the higher the size, the lower the resolution).
27
28 The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigInfo_ and bigWigSummary_.
29
30 .. _bigWigInfo: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigInfo
31 .. _bigWigSummary: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigSummary
32
33 </help>
34 </tool>