Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/FindBoundaryNucleosomes.xml @ 24:a77e126ae856 draft
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| author | timpalpant |
|---|---|
| date | Tue, 19 Jun 2012 22:15:09 -0400 |
| parents | 9d56b5b85740 |
| children | b43c420a6135 |
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| 23:01d5d20eaadd | 24:a77e126ae856 |
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| 1 <tool id="FindNuke" name="Find boundary nucleosomes" version="2.0.0"> | |
| 2 <description>in windows</description> | |
| 3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.FindBoundaryNucleosomes -i $input -l $loci -o $output</command> | |
| 4 <inputs> | |
| 5 <param name="input" type="data" format="tabular" label="Nucleosome calls" /> | |
| 6 <param name="loci" type="data" format="bed,bedgraph,gff" label="List of intervals" /> | |
| 7 </inputs> | |
| 8 <outputs> | |
| 9 <data name="output" format="bed" metadata_source="loci" /> | |
| 10 </outputs> | |
| 11 | |
| 12 <help> | |
| 13 | |
| 14 .. class:: infomark | |
| 15 | |
| 16 Use the Call Nucleosomes tool to create a file of called nucleosomes, then use this tool to identify the first nucleosome's dyad position (peak maximum) from the 5' and 3' end of the gene. | |
| 17 | |
| 18 .. class:: infomark | |
| 19 | |
| 20 **TIP:** Nucleosome calls must be in tabular format of the kind produced by the Nucleosomes -> Call nucleosomes tool. Intervals must be in either Bed, BedGraph, or GFF format. | |
| 21 | |
| 22 ----- | |
| 23 | |
| 24 **Syntax** | |
| 25 | |
| 26 - **Nucleosome calls** is a list of stereotypic nucleosome position calls. | |
| 27 - **List of intervals:** The 5' and 3' boundary nucleosomes will be found for each interval in this list | |
| 28 | |
| 29 </help> | |
| 30 </tool> |