Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/InterpolateDiscontinuousData.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="WigInterpolate" name="Interpolate" version="1.1.0">
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2 <description>missing values in a (Big)Wig file</description>
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3 <command interpreter="sh">galaxyToolRunner.sh converters.InterpolateDiscontinousData -i $input -t $type -m $max -o $output</command>
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4 <inputs>
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5 <param format="bigwig,wig" name="input" type="data" label="Interpolate missing values in" />
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6 <param name="type" type="select" label="Interpolation type">
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7 <option value="nearest">Nearest</option>
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8 <option value="linear">Linear</option>
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9 <option value="cubic">Cubic</option>
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10 </param>
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11 <param name="max" type="integer" value="1000" label="Maximum span of missing values to interpolate (bp)"/>
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12 </inputs>
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13 <outputs>
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14 <data format="wig" name="output" metadata_source="input" />
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15 </outputs>
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16
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17 <help>
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18
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19 This tool will attempt to interpolate missing values (NaN) in a Wig file that result when converting discontinuous microarray probe data to Wig format. Stretches of missing data that extend longer than the allowed maximum will be left as NaN.
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20
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21 -----
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22
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23 **Interpolation types**
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24
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25 - **Nearest** uses the value of the nearest base pair that has data
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26 - **Linear** uses a linear interpolant between the values of the nearest two probes
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27 - **Cubic** uses a cubic interpolant between the values of the nearest two probes
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28
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29 For more information, see Wikipedia_.
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30
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31 .. _Wikipedia: http://en.wikipedia.org/wiki/Interpolation
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32
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33 -----
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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 the Converters -> IntervalToWig tool to convert Bed, BedGraph, or GFF-formatted microarray data to Wig format, then use this tool to interpolate the missing values between probes.
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38
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39 </help>
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40 </tool>