<tool id="intersect_significance" name="intersect_significance">
  <description>significance of two interval sets overlapping</description>
  <command interpreter="python"> bed_overlap_significance.py $fileA $fileB $outfile $outplot $outshuffle $n $genome $fraction $reciprocal </command>
  <inputs>
    <param name="fileA" type="data" format="interval" label="Return intervals in file A" />
    <param name="fileB" type="data" format="interval" label="that overlap with intervals in file B" />
            <param name="genome" type="select" label="Select chromsome size file" >
                <options from_file="chrsize.loc">
                    <column name="name" index="0"/>
                    <column name="value" index="1"/>
                </options>
            </param>
    <param name="fraction" size="10" type="float" value="1e-9" label="Minimum overlap required as a fraction of interval in file A" help="Default is 1E-9 (i.e., 1bp)."/>
 <param name="reciprocal" label="Require that the fraction overlap be reciprocal for A and B" type="boolean" truevalue="-r" falsevalue="" checked="False"/>
    <param name="n" size="10" type="integer" value="100" label="Number of permutations to run" help="File A is shuffled this number of times and the number of random overlaps is used to estimate the null distribution and compute the p value"/>
</inputs>
  <outputs>
    <data format="interval" name="outfile" label="${tool.name} on ${on_string}:overlap"/> 
    <data format="txt" name="outshuffle" label="${tool.name} on ${on_string}:null"/> 
    <data format="pdf" name="outplot" label="${tool.name} on ${on_string}:plot"/> 
  </outputs>
  <help>

**What it does**

This tool uses intersectBed to find intervals in the first dataset that overlap with intervals in the second dataset. To estimate the significance of the overlap, the first dataset is shuffled then intersect with the second dataset to generate a null distribution of the number of overlaps. The tool returns venn diagram plot, histogram of the null distribution, overlapped intervals from the first input, and the null distribution of overlaps. 

  </help>
</tool>