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

Full galaxy wrapper

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rtg/cgmap.xml	Sat Apr 21 21:36:15 2012 -0400
@@ -0,0 +1,36 @@
+<tool id="rtg_cgmap" name="CG map">
+  <description>reads with rtg cg map</description>
+  <command interpreter="bash">galaxy-rtg-map-wrapper.sh paired $output1 $output2 $__new_file_path__ 
+cgmap -t ${template.extra_files_path} 
+--repeat-freq ${repeat}
+-i ${reads.extra_files_path}
+--min-insert-size $minlength --max-insert-size $maxlength
+--max-mated-score $maxscore --max-unmated-score $maxuscore
+</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 mated reads">
+	  <sanitizer sanitize="False"/>
+	</param>
+        <param name="maxuscore" type="text" value="10%" label="Maximum alignment score for umated reads">
+	  <sanitizer sanitize="False"/>
+	</param>
+        <param name="minlength" type="integer" value="0" label="Minimum insert size"/>
+	<param name="maxlength" type="integer" value="1000" label="Maximum insert size"/>
+
+  </inputs>
+  <outputs>
+    <data name="output1" format="samix" label="Cgmap mated on reads data ${reads.hid} and template data ${template.hid}"/>
+    <data name="output2" format="samix" label="Cgmap unmated on reads data ${reads.hid} and template data ${template.hid}"/>
+  </outputs>
+
+  <help>
+This tool performs a NGS read mapping using rtg cgmap
+  </help>
+
+</tool>