Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/FindBoundaryNucleosomes.xml @ 22:727fbba02ef7 draft

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Fix a bug in GeneTrackToWig where +/- strands were not merged correctly. Add option to vary the chunk size of tools that process chromosomes in chunks.
author timpalpant
date Tue, 19 Jun 2012 22:09:23 -0400
parents 9d56b5b85740
children b43c420a6135
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1 <tool id="FindNuke" name="Find boundary nucleosomes" version="2.0.0">
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2 <description>in windows</description>
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3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.FindBoundaryNucleosomes -i $input -l $loci -o $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="tabular" label="Nucleosome calls" />
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6 <param name="loci" type="data" format="bed,bedgraph,gff" label="List of intervals" />
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7 </inputs>
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8 <outputs>
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9 <data name="output" format="bed" metadata_source="loci" />
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10 </outputs>
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11
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12 <help>
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13
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14 .. class:: infomark
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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.
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18 .. class:: infomark
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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.
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22 -----
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24 **Syntax**
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25
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26 - **Nucleosome calls** is a list of stereotypic nucleosome position calls.
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27 - **List of intervals:** The 5' and 3' boundary nucleosomes will be found for each interval in this list
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29 </help>
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30 </tool>