Mercurial > repos > timpalpant > java_genomics_toolkit
diff galaxy-conf/Downsample.xml @ 15:3e477c7e0e73 draft
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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--- a/galaxy-conf/Downsample.xml Sat May 19 10:40:16 2012 -0400 +++ b/galaxy-conf/Downsample.xml Sat Jun 09 16:03:59 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="WigDownsample" name="Downsample" version="1.0.0"> +<tool id="WigDownsample" name="Downsample" version="1.1.0"> <description>a (Big)Wig file</description> <command interpreter="sh">galaxyToolRunner.sh wigmath.Downsample -i $input -m $metric -w $window -o $output</command> <inputs> @@ -16,6 +16,27 @@ <data format="wig" name="output" metadata_source="input" /> </outputs> + <tests> + <test> + <param name="input" value="wigmath1.wig"/> + <param name="window" value="1"/> + <param name="metric" value="mean"/> + <output name="output" file="downsample1.wig"/> + </test> + <test> + <param name="input" value="wigmath2.bw"/> + <param name="window" value="5"/> + <param name="metric" value="max"/> + <output name="output" file="downsample2.wig"/> + </test> + <test> + <param name="input" value="wigmath3.wig"/> + <param name="window" value="100"/> + <param name="metric" value="total"/> + <output name="output" file="downsample3.wig"/> + </test> + </tests> + <help> 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.