<tool id="filterdensity" name="Filter Density" version ="@VERSION@+galaxy1">
  <description>Identify high density positions within indvidual genomes</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code">
      bcftools plugin filter_snv_density $vcf -O b -o $filtered_bcf -- --filename $vcf --region_file $out
      #if $window_size:
      --window_size $window_size
      #end if
      #if $threshold:
      --threshold $threshold
      #end if
  </command>
  <inputs>
    <param name="vcf" type="data" label="Input vcf file" format="vcf" />
    <param name="window_size" type="integer" min="1" label="Size of search window" format="" optional="true"/>
    <param name="threshold"  type="integer"  min="1" label="Density threshold cutoff" format="" optional="true"/>
  </inputs>
  <outputs>
    <data format="txt" name="out" label="High density regions"/>
    <data format="bcf" name="filtered_bcf"/>
  </outputs>
  <tests>
    <test>
    <param name="threshold" value="2"/>
    <param name="window_size" value="100"/>
    <param name="vcf" value="1.vcf"/>
    <output name="out" file="density_regions.txt"/>
    </test>
  </tests>

  <help>
What it does
============

This script will indentify all high density SNV regions in an isolate genome, marking them as filtered-density in the associated bcf, if desired.


Usage
=====

**Parameters**
  - vcf - A vcf file to be analyzed for SNV density.
  - threshold - The threshold distance between SNV's in order for them to be considered 'high density'
  - window_size - The size of the window, in base pairs, that will be looked at at any given time to calculate density.
  </help>
  <expand macro="citations"/>
</tool>