Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/GaussianSmooth.xml @ 21:51b28ce6ef7e draft

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author timpalpant
date Mon, 18 Jun 2012 14:50:31 -0400
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1 <tool id="WigGaussianSmooth" name="Gaussian smooth" version="1.1.0">
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2 <description>a (Big)Wig file</description>
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3 <command interpreter="sh">galaxyToolRunner.sh wigmath.GaussianSmooth -i $input -s $S -o $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="bigwig,wig" label="Smooth the data in" />
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6 <param name="S" type="integer" value="20" optional="true" label="Standard deviation of the Gaussian in base pairs" />
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7 </inputs>
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8 <outputs>
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9 <data format="wig" name="output" metadata_source="input" />
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10 </outputs>
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11 <tests>
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12 <test>
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13 <param name="input" value="wigmath1.wig"/>
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14 <param name="S" value="20"/>
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15 <output name="output" file="gaussian1.wig"/>
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16 </test>
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17 <test>
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18 <param name="input" value="wigmath2.bw"/>
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19 <param name="S" value="3"/>
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20 <output name="output" file="gaussian2.wig"/>
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21 </test>
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22 <test>
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23 <param name="input" value="wigmath3.wig"/>
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24 <param name="S" value="40"/>
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25 <output name="output" file="gaussian3.wig"/>
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26 </test>
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27 </tests>
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28
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29 <help>
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30
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31 This tool smooths genomic data with an area-preserving Gaussian_ filter. The Gaussian filter is computed out to +/- 3 standard deviations.
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32
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33 .. _Gaussian: http://en.wikipedia.org/wiki/Gaussian_filter
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34
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35 .. class:: infomark
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36
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37 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in Wig or BigWig format. Use "edit attributes" to set the correct format if it was not detected correctly.
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38
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39 </help>
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40 </tool>