Mercurial > repos > timpalpant > java_genomics_toolkit

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
14:f58706d4d421 15:3e477c7e0e73
1 <tool id="GaussianSmoother" name="Gaussian smooth" version="1.0.0"> 1 <tool id="WigGaussianSmooth" name="Gaussian smooth" version="1.1.0">
2 <description>a (Big)Wig file</description> 2 <description>a (Big)Wig file</description>
3 <command interpreter="sh">galaxyToolRunner.sh wigmath.GaussianSmooth -i $input -s $S -o $output</command> 3 <command interpreter="sh">galaxyToolRunner.sh wigmath.GaussianSmooth -i $input -s $S -o $output</command>
4 <inputs> 4 <inputs>
5 <param name="input" type="data" format="bigwig,wig" label="Smooth the data in" /> 5 <param name="input" type="data" format="bigwig,wig" label="Smooth the data in" />
6 <param name="S" type="integer" value="20" optional="true" label="Standard deviation of the Gaussian in base pairs" /> 6 <param name="S" type="integer" value="20" optional="true" label="Standard deviation of the Gaussian in base pairs" />
7 </inputs> 7 </inputs>
8 <outputs> 8 <outputs>
9 <data format="wig" name="output" metadata_source="input" /> 9 <data format="wig" name="output" metadata_source="input" />
10 </outputs> 10 </outputs>
11 <tests> 11 <tests>
12 <!--<test> 12 <test>
13 <param name="input" value="test.wig"/> 13 <param name="input" value="wigmath1.wig"/>
14 <param name="dbkey" value="sacCer2"/>
15 <param name="S" value="20"/> 14 <param name="S" value="20"/>
16 <param name="W" value="3"/> 15 <output name="output" file="gaussian1.wig"/>
17 <output name="output" file="smoother.output1"/>
18 </test> 16 </test>
19 <test> 17 <test>
20 <param name="input" value="test.bw"/> 18 <param name="input" value="wigmath2.bw"/>
21 <param name="dbkey" value="sacCer2"/> 19 <param name="S" value="3"/>
22 <param name="S" value="20"/> 20 <output name="output" file="gaussian2.wig"/>
23 <param name="W" value="3"/>
24 <output name="output" file="smoother.output1"/>
25 </test> 21 </test>
26 <test> 22 <test>
27 <param name="input" value="test.wig"/> 23 <param name="input" value="wigmath3.wig"/>
28 <param name="dbkey" value="sacCer2"/> 24 <param name="S" value="40"/>
29 <param name="S" value="10"/> 25 <output name="output" file="gaussian3.wig"/>
30 <param name="W" value="2"/>
31 <output name="output" file="smoother.output2"/>
32 </test> 26 </test>
33 <test>
34 <param name="input" value="test.bw"/>
35 <param name="dbkey" value="sacCer2"/>
36 <param name="S" value="10"/>
37 <param name="W" value="2"/>
38 <output name="output" file="smoother.output2"/>
39 </test>
40 <test>
41 <param name="input" value="test.wig"/>
42 <param name="dbkey" value="sacCer2"/>
43 <param name="S" value="50"/>
44 <param name="W" value="1"/>
45 <output name="output" file="smoother.output3"/>
46 </test>
47 <test>
48 <param name="input" value="test.bw"/>
49 <param name="dbkey" value="sacCer2"/>
50 <param name="S" value="5"/>
51 <param name="W" value="1"/>
52 <output name="output" file="smoother.output3"/>
53 </test>-->
54 </tests> 27 </tests>
55 28
56 <help> 29 <help>
57 30
58 This tool smooths genomic data with an area-preserving Gaussian_ filter. The Gaussian filter is computed out to +/- 3 standard deviations. 31 This tool smooths genomic data with an area-preserving Gaussian_ filter. The Gaussian filter is computed out to +/- 3 standard deviations.