diff mpileupfilteronblastxml/mpileupfilteronblastxml.xml @ 5:26d2c851d48e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mpileupfilteronblastxml/mpileupfilteronblastxml.xml	Mon Jun 16 06:18:07 2014 -0400
@@ -0,0 +1,21 @@
+<tool id="mpileupfilteronblastxml" name="mpileupfilteronblastxml" version="0.03">
+<description>Filter mpileup with blast results</description>
+<command interpreter="perl">
+    mpileupfilteronblastxml.pl -input_variant_file $input_variant_file -input_blastxml_file $input_blastxml_file -window_length $window_length -nb_mismatch_max $nb_mismatch_max > $output_file 
+</command>
+<inputs>
+<param name="input_variant_file"  type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
+<param name="input_blastxml_file"  type="data" format="xml" label="Select a suitable input BLASTXML file from your history"/>
+<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
+<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/>
+</inputs>
+<outputs>
+ <data name="output_file" format="fasta" label="${tool.name} on ${on_string}"/>
+</outputs>
+
+<help>
+
+
+
+</help>
+</tool>