diff tools/rtg/mapx.xml @ 1:8593828f91e7 default tip

Full galaxy wrapper

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rtg/mapx.xml	Sat Apr 21 21:36:15 2012 -0400
@@ -0,0 +1,29 @@
+<tool id="rtg_mapx" name="MapX">
+  <description>protein reads with rtg mapx</description>
+  <command interpreter="bash">galaxy-rtg-mapx-wrapper.sh $output1 $__new_file_path__ 
+mapx -t ${template.extra_files_path} 
+--repeat-freq ${repeat}
+-i ${reads.extra_files_path}
+--max-alignment-score $maxscore
+</command>
+  <inputs>
+    <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
+    <param name="reads" type="data" format="rtg_sdf" label="Reads SDF"/>
+    <param name="repeat" type="text" value="90%" label="Repeat frequency">
+      <sanitizer sanitize="False"/>
+    </param>
+
+	<param name="maxscore" type="text" value="10%" label="Maximum alignment score for reads (percentages do not work ATM)">
+	  <sanitizer sanitize="False"/>
+	</param>
+
+  </inputs>
+  <outputs>
+    <data name="output1" format="tabular" />
+  </outputs>
+
+  <help>
+This tool performs a NGS protein read mapping using rtg mapx
+  </help>
+
+</tool>