Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/ValueDistribution.xml @ 12:81d5b81fb3c2 draft
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
| author | timpalpant |
|---|---|
| date | Wed, 25 Apr 2012 16:53:48 -0400 |
| parents | b1952a90d4bf |
| children | 3e477c7e0e73 |
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| 11:b1952a90d4bf | 12:81d5b81fb3c2 |
|---|---|
| 1 <tool id="ValueDistribution" name="Compute the value distribution" version="1.0.0"> | 1 <tool id="ValueDistribution" name="Compute the value distribution" version="1.0.0"> |
| 2 <description>of a (Big)Wig file</description> | 2 <description>of a (Big)Wig file</description> |
| 3 <command interpreter="sh">galaxyToolRunner.sh wigmath.ValueDistribution -i $input --max $max --min $min -n $bins -o $output</command> | 3 <command interpreter="sh">galaxyToolRunner.sh wigmath.ValueDistribution -i $input |
| 4 #if str( $min ) != '' | |
| 5 --min $min | |
| 6 #end if | |
| 7 | |
| 8 #if str( $max ) != '' | |
| 9 --max $max | |
| 10 #end if | |
| 11 | |
| 12 -n $bins -o $output | |
| 13 </command> | |
| 4 <inputs> | 14 <inputs> |
| 5 <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" /> | 15 <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" /> |
| 6 <param name="min" type="float" optional="true" label="Minimum bin value (optional)" /> | 16 <param name="min" type="float" optional="true" label="Minimum bin value (optional)" /> |
| 7 <param name="max" type="float" optional="true" label="Maximum bin value (optional)" /> | 17 <param name="max" type="float" optional="true" label="Maximum bin value (optional)" /> |
| 8 <param name="bins" type="integer" value="40" label="Number of bins" /> | 18 <param name="bins" type="integer" value="40" label="Number of bins" /> |
| 10 <outputs> | 20 <outputs> |
| 11 <data format="txt" name="output" /> | 21 <data format="txt" name="output" /> |
| 12 </outputs> | 22 </outputs> |
| 13 | 23 |
| 14 <help> | 24 <help> |
| 25 | |
| 26 This tool computes a histogram of the values in a Wig file, as well as the moments of the distribution. | |
| 27 | |
| 28 ----- | |
| 29 | |
| 30 **Syntax** | |
| 31 | |
| 32 - **Input data** is the genomic data used to compute the histogram. | |
| 33 - **Minimum bin value** is the smallest bin. If unset, it is equal to the minimum value in the input data | |
| 34 - **Maximum bin value** is the largest bin. If unset, it is equal to the maximum value in the input data | |
| 35 - **Number of bins** is the number of bins to use. The bin size will be equal to (max - min) / (# bins). | |
| 36 | |
| 37 ----- | |
| 38 | |
| 39 **Output** | |
| 40 | |
| 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 :: | |
| 42 | |
| 43 bin count | |
| 44 <0 3 | |
| 45 0 1 | |
| 46 0.1 10 | |
| 47 0.2 4 | |
| 48 >0.3 12 | |
| 49 | |
| 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). | |
| 51 | |
| 15 </help> | 52 </help> |
| 16 </tool> | 53 </tool> |