Mercurial > repos > xuebing > sharplab_interval_analysis

diff bedclean.xml @ 22:869c7664e584
Uploaded
author: xuebing
date: Sat, 31 Mar 2012 11:52:14 -0400
parents: 783157ce2817
--- a/bedclean.xml	Sat Mar 31 11:49:22 2012 -0400
+++ b/bedclean.xml	Sat Mar 31 11:52:14 2012 -0400
@@ -1,9 +1,35 @@
-<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
-<html><head>
-<title>404 Not Found</title>
-</head><body>
-<h1>Not Found</h1>
-<p>The requested URL /Xwuxbl/bedclean.xml was not found on this server.</p>
-<hr>
-<address>Apache/2.2.14 (Ubuntu) Server at rous.mit.edu Port 80</address>
-</body></html>
+<tool id="bedclean" name="clean interval">
+  <description>remove off-chromosome lines</description>
+  <command interpreter="python">bedclean.py $input $genome $output > $log  </command>
+  <inputs>
+     <param name="input" type="data" format="interval" label="Original interval file"/>
+
+            <param name="genome" type="select" label="Select chromsome size file" >
+                <options from_file="chrsize.loc">
+                    <column name="name" index="0"/>
+                    <column name="value" index="1"/>
+                </options>
+            </param>
+
+  </inputs>
+  <outputs>
+    <data format="input" name="output" label="${tool.name} on ${on_string} (interval)"/>
+    <data format="txt" name="log" label="${tool.name} on ${on_string} (log)"/>
+  </outputs>
+  <help>
+
+**Description**
+
+remove lines that are
+
+1. comment or track name lines
+
+2. on chr*_random
+
+3. or have negative coordinates
+
+4. or the end is larger than chromosome size
+
+
+  </help>
+</tool>