Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/FindBoundaryNucleosomes.xml @ 12:81d5b81fb3c2 draft
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
| author | timpalpant |
|---|---|
| date | Wed, 25 Apr 2012 16:53:48 -0400 |
| parents | b1952a90d4bf |
| children | 3e477c7e0e73 |
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| 11:b1952a90d4bf | 12:81d5b81fb3c2 |
|---|---|
| 1 <tool id="FindNuke" name="Find boundary nucleosomes" version="1.0.0"> | 1 <tool id="FindNuke" name="Find boundary nucleosomes" version="1.0.0"> |
| 2 <description>in windows</description> | 2 <description>in windows</description> |
| 3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.FindBoundaryNucleosomes -i $input -l $loci -o $output</command> | 3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.FindBoundaryNucleosomes -i $input -l $loci -o $output</command> |
| 4 <inputs> | 4 <inputs> |
| 5 <param name="input" type="data" format="nukes" label="Nucleosome calls" /> | 5 <param name="input" type="data" format="tabular" label="Nucleosome calls" /> |
| 6 <param name="loci" type="data" format="bed" label="List of intervals" /> | 6 <param name="loci" type="data" format="bed,bedgraph,gff" label="List of intervals" /> |
| 7 </inputs> | 7 </inputs> |
| 8 <outputs> | 8 <outputs> |
| 9 <data name="output" format="bed" metadata_source="loci" /> | 9 <data name="output" format="bed" metadata_source="loci" /> |
| 10 </outputs> | 10 </outputs> |
| 11 | 11 |
| 12 <help> | 12 <help> |
| 13 .. class:: warningmark | |
| 14 | 13 |
| 15 Use the Call Nucleosomes tool to create a file of called nucleosomes, then use this tool to identify the first nucleosome's dyad position from the 5' or 3' end. | 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 | |
| 16 </help> | 29 </help> |
| 17 </tool> | 30 </tool> |