Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/InterpolateDiscontinuousData.xml @ 16:35031c567ece draft
Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
| author | timpalpant |
|---|---|
| date | Sat, 09 Jun 2012 16:06:25 -0400 |
| parents | 3e477c7e0e73 |
| children |
| rev | line source |
|---|---|
|
15
3e477c7e0e73
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.
timpalpant
parents:
13
diff
changeset
|
1 <tool id="WigInterpolate" name="Interpolate" version="1.1.0"> |
| 13 | 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> |