Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/ValueDistribution.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="WigValueDistribution" name="Compute the value distribution" version="1.1.0">
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2 <description>of a (Big)Wig file</description>
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3 <command interpreter="sh">galaxyToolRunner.sh wigmath.ValueDistribution -i $input
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4 #if str( $min ) != ''
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5 --min $min
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6 #end if
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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( $max ) != ''
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9 --max $max
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10 #end if
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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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12 -n $bins -o $output
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13 </command>
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14 <inputs>
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15 <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" />
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16 <param name="min" type="float" optional="true" label="Minimum bin value (optional)" />
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17 <param name="max" type="float" optional="true" label="Maximum bin value (optional)" />
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18 <param name="bins" type="integer" value="40" label="Number of bins" />
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19 </inputs>
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20 <outputs>
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21 <data format="txt" name="output" />
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22 </outputs>
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23
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24 <help>
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26 This tool computes a histogram of the values in a Wig file, as well as the moments of the distribution.
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28 -----
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30 **Syntax**
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32 - **Input data** is the genomic data used to compute the histogram.
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33 - **Minimum bin value** is the smallest bin. If unset, it is equal to the minimum value in the input data
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34 - **Maximum bin value** is the largest bin. If unset, it is equal to the maximum value in the input data
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35 - **Number of bins** is the number of bins to use. The bin size will be equal to (max - min) / (# bins).
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37 -----
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39 **Output**
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40
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41 The output is in 2-column tabular format, where the first column represents the lower edge of a bin inteval and the second column represents the number of values that fell in that bin. For example if the **minimum bin value** is 0, the **maximum bin value** is 0.3, and the **number of bins** is 3, then the following output might be produced ::
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43 bin count
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44 &lt;0 3
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45 0 1
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46 0.1 10
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47 0.2 4
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48 &gt;0.3 12
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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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50 where there were 3 values in (-inf, 0), 1 value in [0, 0.1), 10 values in [0.1, 0.2), 4 values in [0.2, 0.3), and 12 values in [0.3, inf).
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51
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52 </help>
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53 </tool>