<tool id="PredictFAIRE" name="Predict FAIRE signal" version="1.1.0">
  <description>from nucleosome occupancy</description>
  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.PredictFAIRESignal -i $input -s $sonication -c $crosslinking -x $extend -o $output</command>
  <inputs>
      <param format="bigwig,wig" name="input" type="data" label="Nucleosome occupancy data" />
      <param format="tabular" name="sonication" type="data" label="Sonication fragment length distribution" />
      <param name="crosslinking" type="float" value="1.0" label="Crosslinking coefficient" />
      <param name="extend" type="integer" value="250" label="In silico read extension (-1 for paired-end mode)" />
  </inputs>
  <outputs>
      <data format="wig" name="output" metadata_source="input" />
  </outputs>
  
  <help>
    
This tool attempts to predict FAIRE signal from nucleosome occupancy by calculating the probability that a random sonicated fragment is occupied anywhere by a nucleosome.

-----

**Syntax**

- **Nucleosome occupancy data** should be fragment coverage data from an MNase-seq experiment
- **Sonication fragment length distribution:** The relative proportion of each size of fragment produced by sonication
- **Crosslinking coefficient** is the efficiency of crosslinking (what fraction of the time is a nucleosome crosslinked)
- **In silico read extension** is the length that single-end reads should be extended to match FAIRE-seq data

-----

Sonication fragment distribution must be provided in the following tabular format ::

  length  proportion
  
So for example ::

  1  0.1
  2  0.2
  3  0.3
  4  0.2
  5  0.2
    
  </help>
</tool>