Mercurial > repos > xuebing > sharplabtool

diff convertEnsembl.xml @ 11:b7f1d9f8f3bc

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author xuebing
date Sat, 10 Mar 2012 07:59:27 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convertEnsembl.xml	Sat Mar 10 07:59:27 2012 -0500
@@ -0,0 +1,18 @@
+<tool id="convertens" name="convert ensembl">
+  <description>to ucsc</description>
+  <command interpreter="python">convertEnsembl.py $input $output $skip  </command>
+  <inputs>
+    <param name="input" format="interval" type="data" label="Original file"/>
+    <param name="skip" size="10" type="integer" value="0" label="Number of beginning lines to skip"/>
+  </inputs>
+  <outputs>
+    <data format="input" name="output" />
+  </outputs>
+  <help>
+
+**What it does**
+
+This tool convert ensembl based interval file to ucsc format: add 'chr' to chromosome number (column 1), and replace '1' and '-1' with '+' and '-' in column 6, respectively. 
+
+ </help>
+</tool>