Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/FindBoundaryNucleosomes.xml @ 24:a77e126ae856 draft
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author | timpalpant |
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date | Tue, 19 Jun 2012 22:15:09 -0400 |
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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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15 |
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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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17 |
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18 .. class:: infomark |
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19 |
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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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21 |
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22 ----- |
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23 |
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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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28 |
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29 </help> |
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30 </tool> |