Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/ZScore.xml @ 16:35031c567ece draft

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Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
author timpalpant
date Sat, 09 Jun 2012 16:06:25 -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="WigZScore" name="Z-Score" version="1.2.0">
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2 <description>a (Big)Wig file</description>
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3 <command interpreter="sh">galaxyToolRunner.sh wigmath.ZScore -i $input $chr -o $output</command>
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4 <inputs>
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5 <param format="bigwig,wig" name="input" type="data" label="Z-score the data in" />
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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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6 <param name="chr" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Z-score chromosomes individually" />
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7 </inputs>
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8 <outputs>
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9 <data format="wig" name="output" metadata_source="input" />
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10 </outputs>
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11 <tests>
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12 <test>
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13 <param name="input" value="wigmath1.wig"/>
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14 <output name="output" file="zscorer1.wig"/>
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15 </test>
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16 <test>
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17 <param name="input" value="wigmath2.wig"/>
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18 <output name="output" file="zscorer2.wig"/>
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19 </test>
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20 <test>
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21 <param name="input" value="wigmath3.wig"/>
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22 <output name="output" file="zscorer3.wig"/>
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23 </test>
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24 <test>
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25 <param name="input" value="wigmath1.bw"/>
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26 <output name="output" file="zscorer4.wig"/>
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27 </test>
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28 <test>
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29 <param name="input" value="wigmath2.bw"/>
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30 <output name="output" file="zscorer5.wig"/>
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31 </test>
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32 <test>
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33 <param name="input" value="wigmath3.bw"/>
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34 <output name="output" file="zscorer6.wig"/>
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35 </test>
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36 </tests>
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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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38 <help>
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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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40 This tool will compute normal scores (Z-scores) for each of the values in a Wig file. For each base pair, the Z-scored value is equal to the deviance from the mean divided by the standard deviation (i.e. the number of standard deviations a value is away from the mean). The output file should have mean 0 and standard deviation 1.
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42 .. class:: infomark
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44 This tool is equivalent to using the **Mean Shift** tool to shift a Wig file to mean 0, then using the **Scale** tool to scale by 1/(standard deviation).
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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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46 .. class:: infomark
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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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48 **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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50 </help>
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51 </tool>