diff snpSift_vartype.xml @ 3:20c7d583fec1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5

--- a/snpSift_vartype.xml	Mon Dec 05 12:11:18 2016 -0500
+++ b/snpSift_vartype.xml	Mon Jun 12 10:25:32 2017 -0400
@@ -7,16 +7,17 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        @CONDA_SNPSIFT_JAR_PATH@ &&
-        java -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output"
-]]>
-    </command>
+SnpSift varType
+'$input'
+2> '$log'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="vcf" name="input" type="data" label="Variant file (VCF)"/>
+        <param name="input" type="data" format="vcf" 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 ${on_string}: log" />
+        <data name="output" format="vcf" label="${tool.name} on ${on_string}: VCF" />
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: log" />
     </outputs>
     <tests>
     </tests>
@@ -35,7 +36,6 @@
 
 .. _CRS4 Srl.: http://www.crs4.it/
 .. _MIT license: https://opensource.org/licenses/MIT
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>