diff rapsodyn/ParseBlastForUniqueMatch.xml @ 0:442a7c88b886 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/ParseBlastForUniqueMatch.xml	Wed Sep 10 09:18:15 2014 -0400
@@ -0,0 +1,21 @@
+<tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="0.01">
+<description>Filter mpileup with blast results</description>
+<command interpreter="perl">
+    ParseBlastForUniqueMatch.pl $input_variant_file $input_blast_file $window_length $nb_mismatch_max > $output_file 
+</command>
+<inputs>
+<param name="input_variant_file"  type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
+<param name="input_blast_file"  type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/>
+<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
+<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/>
+</inputs>
+<outputs>
+ <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
+</outputs>
+
+<help>
+
+
+
+</help>
+</tool>