Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/GaussianSmooth.xml @ 15:3e477c7e0e73 draft

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Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
author timpalpant
date Sat, 09 Jun 2012 16:03:59 -0400
parents 81d5b81fb3c2
children
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3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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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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3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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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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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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33 .. _Gaussian: http://en.wikipedia.org/wiki/Gaussian_filter
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35 .. class:: infomark
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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>