diff intersect_snp.xml @ 0:3edc7bb490d3 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/intersect_snp.xml	Thu Nov 08 12:56:30 2018 -0500
@@ -0,0 +1,41 @@
+<tool id="intersect_snp" name="intersect_snp" version="0">
+  <description>tool for snp VCF file intersection </description>
+  <requirements>
+  </requirements>
+  <command>
+	perl  $__tool_directory__/14_june_18_intersect.snps.with.infos.pl
+  $input1 $input2 $input3 intersect 2>log
+  </command>
+  <inputs>
+    <param name="input1" format="vcf" type="data" label="VCF File" help="Varscan2 snp output" />
+    <param name="input2" format="vcf" type="data" label="VCF File" help="Frebayes snp output" />
+    <param name="input3" format="vcf" type="data" label="VCF File" help="GATK HaplotypeCaller snp output" />
+  </inputs>
+  <outputs>
+    <data format="vcf" name="output1" from_work_dir="intersect.common.snps.vcf" label="${tool.name} on ${on_string} common snps" />
+    <data format="vcf" name="output2" from_work_dir="intersect.unique.snps.vcf" label="${tool.name} on ${on_string} unique snps" />
+    <data format="txt" name="output3" from_work_dir="log" label="${tool.name} on ${on_string} log" />
+  </outputs>
+  <stdio>
+  </stdio>
+  <help>
+**WHAT IT DOES**
+
+Predictions of SNPs 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:**
+
+-SNPs common to at least 2 methods
+
+-Singleton SNPs obtained from a single method
+
+  </help>
+  <citations>
+       <citation type="doi">10.1186/s12864-018-4508-1</citation>
+  </citations>
+  <tests>
+    <test>
+    </test>
+  </tests>
+
+</tool>