comparison galaxy-conf/InterpolateDiscontinuousData.xml @ 24:a77e126ae856 draft

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author timpalpant
date Tue, 19 Jun 2012 22:15:09 -0400
parents 9d56b5b85740
children b43c420a6135
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23:01d5d20eaadd 24:a77e126ae856
1 <tool id="WigInterpolate" name="Interpolate" version="1.1.0">
2 <description>missing values in a (Big)Wig file</description>
3 <command interpreter="sh">galaxyToolRunner.sh converters.InterpolateDiscontinousData -i $input -t $type -m $max -o $output</command>
4 <inputs>
5 <param format="bigwig,wig" name="input" type="data" label="Interpolate missing values in" />
6 <param name="type" type="select" label="Interpolation type">
7 <option value="nearest">Nearest</option>
8 <option value="linear">Linear</option>
9 <option value="cubic">Cubic</option>
10 </param>
11 <param name="max" type="integer" value="1000" label="Maximum span of missing values to interpolate (bp)"/>
12 </inputs>
13 <outputs>
14 <data format="wig" name="output" metadata_source="input" />
15 </outputs>
16
17 <help>
18
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.
20
21 -----
22
23 **Interpolation types**
24
25 - **Nearest** uses the value of the nearest base pair that has data
26 - **Linear** uses a linear interpolant between the values of the nearest two probes
27 - **Cubic** uses a cubic interpolant between the values of the nearest two probes
28
29 For more information, see Wikipedia_.
30
31 .. _Wikipedia: http://en.wikipedia.org/wiki/Interpolation
32
33 -----
34
35 .. class:: infomark
36
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.
38
39 </help>
40 </tool>