Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/PredictFAIRESignal.xml @ 17:ace7855c1017 draft

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Add back tool_data_table_conf.xml.sample since apparently it's still needed.
author timpalpant
date Sat, 09 Jun 2012 16:10:42 -0400
parents 3e477c7e0e73
children
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3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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1 <tool id="PredictFAIRE" name="Predict FAIRE signal" version="1.1.0">
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2 <description>from nucleosome occupancy</description>
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3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.PredictFAIRESignal -i $input -s $sonication -c $crosslinking -x $extend -o $output</command>
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4 <inputs>
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5 <param format="bigwig,wig" name="input" type="data" label="Nucleosome occupancy data" />
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6 <param format="tabular" name="sonication" type="data" label="Sonication fragment length distribution" />
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7 <param name="crosslinking" type="float" value="1.0" label="Crosslinking coefficient" />
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3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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8 <param name="extend" type="integer" value="250" label="In silico read extension (-1 for paired-end mode)" />
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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9 </inputs>
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10 <outputs>
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11 <data format="wig" name="output" metadata_source="input" />
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12 </outputs>
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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14 <help>
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16 This tool attempts to predict FAIRE signal from nucleosome occupancy by calculating the probability that a random sonicated fragment is occupied anywhere by a nucleosome.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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18 -----
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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20 **Syntax**
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22 - **Nucleosome occupancy data** should be fragment coverage data from an MNase-seq experiment
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23 - **Sonication fragment length distribution:** The relative proportion of each size of fragment produced by sonication
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24 - **Crosslinking coefficient** is the efficiency of crosslinking (what fraction of the time is a nucleosome crosslinked)
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25 - **In silico read extension** is the length that single-end reads should be extended to match FAIRE-seq data
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27 -----
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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29 Sonication fragment distribution must be provided in the following tabular format ::
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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31 length proportion
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33 So for example ::
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35 1 0.1
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36 2 0.2
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37 3 0.3
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38 4 0.2
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39 5 0.2
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41 </help>
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42 </tool>