<tool id="intersect_indels" name="intersect_indels" version="1">
  <description>tool for indel VCF file intersection </description>
  <requirements>
  </requirements>
  <command>
	perl  $__tool_directory__/14_june_18_intersect.indels.with.infos.pl
  $input1 $input2 $input3 intersect 2>log
  </command>
  <inputs>
    <param name="input1" format="vcf" type="data" label="VCF File" help="Varscan2 indels output" />
    <param name="input2" format="vcf" type="data" label="VCF File" help="Frebayes indels output" />
    <param name="input3" format="vcf" type="data" label="VCF File" help="GATK HaplotypeCaller indels output" />
  </inputs>
  <outputs>
    <data format="vcf" name="output1" from_work_dir="intersect.common.indels.vcf" label="${tool.name} on ${on_string} common indels" />
    <data format="vcf" name="output2" from_work_dir="intersect.unique.indels.vcf" label="${tool.name} on ${on_string} unique indels" />
    <data format="txt" name="output3" from_work_dir="log" label="${tool.name} on ${on_string} log" />
  </outputs>
  <stdio>
  </stdio>
  <help>
**WHAT IT DOES**

Predictions of indels from Varscan2, GATK and Freebayes are consolidated into a single call-set following a simple majority consensus rule. Variants  identified by at least two methods are incorporated into a final “high confidence” call set.Singleton variants predicted by only one method are considered less reliable and are included in a low quality call-set.

**The final output consists in two VCF files:**

-INDELs common to at least 2 methods

-Singleton INDELs obtained from a single method

  </help>
  <citations>
	<citation type="doi">10.1186/s12864-018-4508-1</citation>
  </citations>
  <tests>
    <test>
    </test>
  </tests>

</tool>