Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/Phasogram.xml @ 25:b43c420a6135 draft default tip

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Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
author timpalpant
date Sat, 09 Feb 2019 14:02:24 -0500
parents 9d56b5b85740
children
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1 <tool id="Phasogram" name="Make phasogram" version="1.0.0">
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2 <description>of dyads</description>
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b43c420a6135 Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
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3 <command interpreter="bash">galaxyToolRunner.sh nucleosomes.Phasogram -i $input -m $max -o $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="bigwig,wig" label="Dyads (Big)Wig file" />
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6 <param name="max" type="integer" value="1000" label="Maximum phase shift (bp)" />
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7 </inputs>
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8 <outputs>
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9 <data name="output" format="tabular" />
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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 This tool calculates the phase distribution of sequencing data. It can be used to identify genome-wide periodicities. Phase counts are aggregated for each base pair across the genome. This is equivalent to summing the autocovariance of a sliding window across the genome. The tool is a reimplementation of the algorithm described in (Valouev et al. 2011).
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16 .. class:: infomark
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18 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in Wig or BigWig format. Use "edit attributes" to set the correct format if it was not detected correctly.
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20 -----
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22 **Citation**
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24 Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ and Sidow A (2011) Determinants of nucleosome organization in primary human cells. Nature 474: 516–520
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26 </help>
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27 </tool>