comparison galaxy-conf/ValueDistribution.xml @ 20:9d56b5b85740 draft

Reuploaded to see if tools get loaded correctly this time.

20:9d56b5b85740

<tool id="WigValueDistribution" name="Compute the value distribution" version="1.1.0">
  <description>of a (Big)Wig file</description>
  <command interpreter="sh">galaxyToolRunner.sh wigmath.ValueDistribution -i $input 
    #if str( $min ) != ''
      --min $min
    #end if
    
    #if str( $max ) != ''
      --max $max
    #end if
    
    -n $bins -o $output
  </command>
  <inputs>
      <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" />
      <param name="min" type="float" optional="true" label="Minimum bin value (optional)" />
      <param name="max" type="float" optional="true" label="Maximum bin value (optional)" />
      <param name="bins" type="integer" value="40" label="Number of bins" />
  </inputs>
  <outputs>
      <data format="txt" name="output" />
  </outputs>
  
<help>
  
This tool computes a histogram of the values in a Wig file, as well as the moments of the distribution.

-----

**Syntax**

- **Input data** is the genomic data used to compute the histogram.
- **Minimum bin value** is the smallest bin. If unset, it is equal to the minimum value in the input data
- **Maximum bin value** is the largest bin. If unset, it is equal to the maximum value in the input data
- **Number of bins** is the number of bins to use. The bin size will be equal to (max - min) / (# bins).

-----

**Output**

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 ::

  bin       count
  &lt;0        3
  0         1
  0.1       10
  0.2       4
  &gt;0.3      12
  
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).
  
</help>
</tool>