Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/ExtractDataFromRegion.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 | |
| children | b43c420a6135 |
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| 14:f58706d4d421 | 15:3e477c7e0e73 |
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| 1 <tool id="ExtractDataFromWig" name="Extract data from a Wig file" version="1.0.0"> | |
| 2 <description>for a genomic interval</description> | |
| 3 <command interpreter="sh"> | |
| 4 galaxyToolRunner.sh ngs.ExtractDataFromRegion --chr $chr --start $start --stop $stop -o $output $file1 | |
| 5 #for $input in $inputs | |
| 6 ${input.file} | |
| 7 #end for | |
| 8 </command> | |
| 9 <inputs> | |
| 10 <param name="file1" label="(Big)Wig file" type="data" format="bigwig,wig" /> | |
| 11 <repeat name="inputs" title="(Big)Wig file"> | |
| 12 <param name="file" type="data" format="bigwig,wig" /> | |
| 13 </repeat> | |
| 14 <param name="chr" type="text" label="Chromosome" /> | |
| 15 <param name="start" type="integer" value="1" label="Start base pair" /> | |
| 16 <param name="stop" type="integer" value="1000" label="Stop base pair" /> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="tabular" name="output" /> | |
| 20 </outputs> | |
| 21 | |
| 22 <help> | |
| 23 | |
| 24 This tool will extract data from Wig or BigWig file(s) for a specific region of the genome. | |
| 25 | |
| 26 </help> | |
| 27 </tool> |