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comparison galaxy-conf/Downsample.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 eb53be9a09f4
children
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14:f58706d4d421 15:3e477c7e0e73
1 <tool id="WigDownsample" name="Downsample" version="1.0.0"> 1 <tool id="WigDownsample" name="Downsample" 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.Downsample -i $input -m $metric -w $window -o $output</command> 3 <command interpreter="sh">galaxyToolRunner.sh wigmath.Downsample -i $input -m $metric -w $window -o $output</command>
4 <inputs> 4 <inputs>
5 <param format="bigwig,wig" name="input" type="data" label="Original data" /> 5 <param format="bigwig,wig" name="input" type="data" label="Original data" />
6 <param name="window" type="integer" value="100" label="Window size (bp)" /> 6 <param name="window" type="integer" value="100" label="Window size (bp)" />
13 </param> 13 </param>
14 </inputs> 14 </inputs>
15 <outputs> 15 <outputs>
16 <data format="wig" name="output" metadata_source="input" /> 16 <data format="wig" name="output" metadata_source="input" />
17 </outputs> 17 </outputs>
18
19 <tests>
20 <test>
21 <param name="input" value="wigmath1.wig"/>
22 <param name="window" value="1"/>
23 <param name="metric" value="mean"/>
24 <output name="output" file="downsample1.wig"/>
25 </test>
26 <test>
27 <param name="input" value="wigmath2.bw"/>
28 <param name="window" value="5"/>
29 <param name="metric" value="max"/>
30 <output name="output" file="downsample2.wig"/>
31 </test>
32 <test>
33 <param name="input" value="wigmath3.wig"/>
34 <param name="window" value="100"/>
35 <param name="metric" value="total"/>
36 <output name="output" file="downsample3.wig"/>
37 </test>
38 </tests>
18 39
19 <help> 40 <help>
20 41
21 This tool can be used to reduce the resolution and file size of Wig files for easier upload to UCSC. Data is downsampled in non-overlapping windows starting from the beginning of each chromosome. Each window can be downsampled as the mean, minimum, maximum, total, or coverage of the original data. 42 This tool can be used to reduce the resolution and file size of Wig files for easier upload to UCSC. Data is downsampled in non-overlapping windows starting from the beginning of each chromosome. Each window can be downsampled as the mean, minimum, maximum, total, or coverage of the original data.
22 43