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

Full galaxy wrapper

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rtg/snpsim.xml	Sat Apr 21 21:36:15 2012 -0400
@@ -0,0 +1,30 @@
+<tool id="rtg_snpsim" name="Simulate SNPs">
+  <description>with rtg snpsim</description>
+  <command interpreter="bash">galaxy-rtg-snpsim-wrapper.sh ${output3} ${output3.extra_files_path} snpsim
+ --seed $seed -i ${input.extra_files_path} 
+-o ${output.extra_files_path}
+#if $str($diploid) == "true":
+-O ${output2.extra_files_path}
+#end if
+>$output</command>
+  <inputs>
+    <param name="input" type="data" format="rtg_sdf" label="SDF containing input genome"/>
+    <param name="diploid" type="select" label="Generate diploid mutations">
+      <option value="true">Yes</option>
+      <option value="false" selected="true">No</option>
+    </param>
+    <param name="seed" type="integer" value="42" label="Seed" help="Seed for the random number generator"/>
+  </inputs>
+  <outputs>
+    <data format="rtg_sdf" name="output" label="Mutated genome on data ${input.hid}"/>
+    <data format="rtg_sdf" name="output2" label="Second mutated genome on data ${input.hid}">
+      <filter>diploid == "true"</filter>
+    </data>
+    <data format="vcf" name="output3" label="SNPs file generated on data ${input.hid}" />
+  </outputs>
+
+  <help>
+This tool creates a simulated mutation of a reference genome. Can generate either haploid or diploid mutations.
+  </help>
+
+</tool>