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annotate galaxy-conf/DynaPro.xml @ 15:3e477c7e0e73 draft

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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.
author timpalpant
date Sat, 09 Jun 2012 16:03:59 -0400
parents 81d5b81fb3c2
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="DynaPro" name="Compute equilibrium nucleosome positions" version="1.1.0">
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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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2 <description>using DynaPro</description>
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3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.DynaPro -i $input -n $N
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4 #if str( $mean ) != ''
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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5 -m $mean
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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6 #end if
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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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8 #if str( $variance ) != ''
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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9 -v $variance
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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10 #end if
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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11 -o $output
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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12 </command>
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13 <inputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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14 <param format="bigwig,wig" name="input" type="data" label="Energy landscape" />
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15 <param name="N" type="integer" value="147" label="Nucleosome size (bp)" />
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16 <param name="mean" type="float" optional="true" label="Shift energy landscape to have mean" />
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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17 <param name="variance" type="float" optional="true" label="Rescale energy landscape to have variance" />
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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18 </inputs>
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19 <outputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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20 <data format="wig" name="output" metadata_source="input" />
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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21 </outputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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22 <help>
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24 .. class:: warningmark
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26 At present, this tool is only suitable for small genomes (yeast) since entire chromosomes must be loaded into memory.
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28 -----
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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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30 Equilibrium nucleosome distribution is modeled as a one-dimensional fluid of hard rods adsorbing and moving within an external potential. This tool provides a simplified version of the DynaPro_ algorithm for a single factor interacting with hard-core repulsion.
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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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32 .. _DynaPro: http://nucleosome.rutgers.edu/nucleosome/
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34 -----
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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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36 **Syntax**
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37
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38 - **Energy landscape** is the external potential function for each genomic base pair, and must be in Wig format.
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39 - **Nucleosome size** is the hard-core interaction size.
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41 -----
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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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43 **Citation**
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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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45 Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J and Siggia ED (2009) Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucleic Acids Res 37: 4707–4722.
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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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47 </help>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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48 </tool>