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diff synteny_parse.xml @ 2:ea73705ac0f6 draft default tip

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author cschu
date Wed, 01 Apr 2015 05:36:10 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/synteny_parse.xml	Wed Apr 01 05:36:10 2015 -0400
@@ -0,0 +1,30 @@
+<tool id="synteny_parse" name="synteny_parse">
+	<description>Parse synteny information from BlastXML.</description>
+	<requirements>
+	  <!-- <requirement type="package" version="2.7.4">python</requirement>	  -->
+	  <requirement type="package" version="1.65">biopython</requirement>
+          <requirement type="python-module">Bio</requirement>               	
+          <requirement type="python-module">Bio.Blast</requirement>               	
+        </requirements>
+	<command interpreter="python">synteny_parse.py
+		--evalue="${minE.value}"
+		--min-identity="${minID.value}"
+		--min-query-coverage="${minQCOV.value}"		
+		$blastXML_in $out
+		</command>
+	<inputs>
+		<param name="blastXML_in" type="data" format="xml" label="BLAST xml output" />
+		<param name="minE" type="float" value="1e-10" label="e-value cutoff" />
+		<param name="minID" type="float" value="0.75" label="identity cutoff" />
+		<param name="minQCOV" type="float" value="0.75" label="query-coverage cutoff" />
+ amino acid sequences" />
+	</inputs>
+	<outputs>
+		<data format="tabular" name="out" label="Filtered Blast results ${on_string}" />
+	</outputs>
+
+	<help>
+		This tool does stuff.
+	</help>
+</tool>
+