Mercurial > repos > diego > rtg_investigator

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

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Full galaxy wrapper
author diego
date Sat, 21 Apr 2012 21:36:15 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rtg/coverage.xml	Sat Apr 21 21:36:15 2012 -0400
@@ -0,0 +1,26 @@
+<tool id="rtg_coverage" name="Coverage">
+  <description>coverage</description>
+  <command interpreter="bash">galaxy-rtg-singleoutput-wrapper.sh $output $output.id $__new_file_path__ coverage.bed
+coverage -t ${template.extra_files_path} 
+$input1
+#for $i in $inputs
+  ${i.input}
+#end for
+-Z
+</command>
+  <inputs>
+    <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
+    <param name="input1" label="First SAM file" type="data" format="sam,samix" />
+    <repeat name="inputs" title="Input SAM Files">
+      <param name="input" label="Add file" type="data" format="sam,samix" />
+    </repeat>
+  </inputs>
+  <outputs>
+    <data name="output" format="bed"/>
+  </outputs>
+
+  <help>
+This tool calculates coverage using rtg coverage 
+  </help>
+
+</tool>