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

Full galaxy wrapper

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rtg/cgsim.xml	Sat Apr 21 21:36:15 2012 -0400
@@ -0,0 +1,43 @@
+<tool id="rtg_cgsim" name="Simulate CG reads">
+  <description>with RTG cgsim</description>
+  <command interpreter="bash">galaxy-rtg-wrapper.sh cgsim
+-t ${input.extra_files_path}
+#if $limit.sType == "numreads":
+-n $limit.n
+#else
+-c $limit.c
+#end if
+-m $m
+-M $M
+--seed $seed
+-o ${output.extra_files_path} >$output</command>
+  <inputs>
+
+    <param name="input" type="data" format="rtg_sdf" label="Source SDF"/>
+    <param name="m" type="integer" value="350" label="Minimum fragment length" help=""/>
+    <param name="M" type="integer" value="500" label="Maximum fragment length" help=""/>
+
+    <conditional name="limit">
+      <param name="sType" type="select" label="Select read limit">
+        <option value="numreads">Fixed number of reads</option>
+        <option value="coverage">Fixed coverage</option>
+      </param>
+      <when value="numreads">
+        <param name="n" type="integer" value="1000" label="Number of reads" help="Total number of reads"/>
+      </when>
+      <when value="coverage">
+        <param name="c" type="float" value="1" label="Coverage" help="Total coverage"/>
+      </when>
+    </conditional>	
+
+    <param name="seed" type="integer" label="Seed" value="42" help="Seed for the random number generator"/>
+  </inputs>
+  <outputs>
+    <data format="rtg_sdf" name="output" />
+  </outputs>
+
+  <help>
+This tool creates an SDF containing randomly generated CG reads.
+  </help>
+
+</tool>