# HG changeset patch
# User xuebing
# Date 1331385044 18000
# Node ID 2f4ea569f04838b6b6db6256f351e77b90836a30
# Parent  b7f1d9f8f3bc7d7450e082aaba983f9f45d780d3
Uploaded

diff -r b7f1d9f8f3bc -r 2f4ea569f048 bedclean.xml
--- a/bedclean.xml	Sat Mar 10 07:59:27 2012 -0500
+++ b/bedclean.xml	Sat Mar 10 08:10:44 2012 -0500
@@ -1,33 +1,33 @@
 <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 genome">
-     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
-     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
-     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
-     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
+  <command interpreter="python">bedClean.py $input $genome $output > $log  </command>
+  <inputs>
+     <param name="input" type="data" format="interval" label="Original interval file"/>
+    <param name="genome" type="select" label="Select genome">
+     <option value="/media/data/Research/Project/galaxy/data/chrsize/mouse.mm9.genome" selected="true">mm9</option>
+     <option value="/media/data/Research/Project/galaxy/data/chrsize/mouse.mm8.genome">mm8</option>
+     <option value="/media/data/Research/Project/galaxy/data/chrsize/human.hg18.genome">hg18</option>
+     <option value="/media/data/Research/Project/galaxy/data/chrsize/human.hg19.genome">hg19</option>
     </param>
   </inputs>
   <outputs>
-    <data format="input" name="output" label="${tool.name} on ${on_string} (interval)"/>
+    <data format="input" name="output" label="${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
-
+**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>