diff snpSift_vartype.xml @ 4:baf6602903e1

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpSift_vartype.xml	Wed Dec 09 14:03:26 2015 -0500
@@ -0,0 +1,43 @@
+<tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.0">
+    <description>Annotate with variant type</description>
+    <macros>
+        <import>snpSift_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
+        java -jar \$SNPEFF_JAR_PATH/SnpSift.jar varType $input 2> $log > $output
+]]>
+    </command>
+    <inputs>
+        <param format="vcf" name="input" type="data" label="Variant file (VCF)"/>
+    </inputs>
+    <outputs>
+        <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" />
+        <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool uses `SnpSift Variant type`_ to add the variant type (SNP/MNP/INS/DEL/MIXED) in the INFO field. It also adds "HOM/HET", but this last one works if there is only one sample (otherwise it doesn't make any sense).
+
+.. _SnpSift Variant type: http://snpeff.sourceforge.net/SnpSift.html#VariantType
+
+------
+
+**License**
+
+This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
+
+.. _CRS4 Srl.: http://www.crs4.it/
+.. _MIT license: http://opensource.org/licenses/MIT
+
+@CITATION_SECTION@
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>