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1 <tool id="bigwig_to_wig" name="BigWig to Wig" version="1.0.2">
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2 <description>converter</description>
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2
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3 <command interpreter="bash">bigwig_to_wig.sh -f $input -b $bin_size -l $mylab > $output </command>
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4 <requirements>
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5 <requirement type="package" version="1.0">bigWigSummary</requirement>
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6 <requirement type="package" version="1.0">bigWigInfo</requirement>
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7 </requirements>
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8 <inputs>
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9 <param format="bigwig" name="input" type="data" label="BigWig file to convert" />
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10 <param name="bin_size" size="4" type="integer" value="500" label="Bin size" help="Must be an even integer > 100." />
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11 <param name="mylab" type="text" value="wiggle_file" label="Output file prefix" help="" />
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12 </inputs>
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13 <outputs>
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14 <data format="wig" name="output" label="${mylab}_density_bin${bin_size}.wig" />
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="input" value="1.bigwig" />
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19 <param name="bin_size" value="500" />
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20 <output name="output" file="1.wig" />
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21 </test>
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22 </tests>
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23 <help>
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24
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25 This tool converts a **BigWig** file to fixed step **Wiggle** format.
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26 Resolution is controlled through the bin size (the higher the size, the lower the resolution).
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27
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28 The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigInfo_ and bigWigSummary_.
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29
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30 .. _bigWigInfo: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigInfo
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31 .. _bigWigSummary: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigSummary
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32
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33 </help>
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34 </tool>
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