--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/intersect_indels.xml	Thu Nov 08 12:54:29 2018 -0500
@@ -0,0 +1,41 @@
+<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>