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

Full galaxy wrapper

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rtg/mapf.xml	Sat Apr 21 21:36:15 2012 -0400
@@ -0,0 +1,53 @@
+<tool id="rtg_mapf" name="Mapf">
+  <description>reads with rtg mapf</description>
+  <command interpreter="bash">galaxy-rtg-map-wrapper.sh $paired.sPaired $output1 $output2 $__new_file_path__ 
+mapf -t ${template.extra_files_path} 
+--repeat-freq ${repeat}
+-i ${reads.extra_files_path}
+#if $paired.sPaired == "paired":
+--min-insert-size $paired.minlength --max-insert-size $paired.maxlength
+--max-mated-score $paired.maxscore --max-unmated-score $paired.maxuscore
+#else:
+--max-alignment-score $paired.maxscore
+#end if
+--sam
+</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>
+
+    <conditional name="paired">
+      <param name="sPaired" type="select" label="Are you mapping paired-end reads?">
+        <option value="paired">Paired-end</option>
+        <option value="single">Single-end</option>
+      </param>
+      <when value="single">
+	<param name="maxscore" type="text" value="10%" label="Maximum alignment score for reads (percentages do not work ATM)">
+	  <sanitizer sanitize="False"/>
+	</param>
+      </when>
+      <when value="paired">
+	<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="200" label="Minimum insert size"/>
+	<param name="maxlength" type="integer" value="400" label="Maximum insert size"/>
+      </when>
+    </conditional>	
+
+  </inputs>
+  <outputs>
+    <data name="output1" format="samix" />
+  </outputs>
+
+  <help>
+This tool filters reads for contaminant sequences by mapping them against the contaminant template using rtg mapf
+  </help>
+
+</tool>