# HG changeset patch
# User xuebing
# Date 1333216725 14400
# Node ID bac957616de74c58bafda0c4a72c23d03308ce21
# Parent  d445743c65bf359bac09a22b12299ca46d935ba8
Uploaded

diff -r d445743c65bf -r bac957616de7 bed_shuffle.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bed_shuffle.xml	Sat Mar 31 13:58:45 2012 -0400
@@ -0,0 +1,44 @@
+<tool id="bed_shuffle" name="bed_shuffle">
+  <description>shuffle intervals chromosome not weighted by length</description>
+  <command>shuffleBed -i $input -g $genome $chrom > $outfile 
+    #if $limit.limit_select=="include":
+    -incl $limitfile
+    #else if $limit.limit_select=="exclude":
+    -excl $limitfile 
+    #end if
+  </command>
+  <inputs>
+    <param name="input" format="bed,gff,vcf" type="data" label="Original intervals (BED/GFF/VCF)" />
+           <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>
+
+    <param name="chrom" label="keep intervals on the same chromosome?" type="boolean" truevalue="-chrom" falsevalue="" checked="False"/>
+    <conditional name="limit">
+    	<param name="limit_select" type="select" label="restrictions for the shuffling" help="Instead of randomly placing features in a genome, one can specify regions features should or should not be randomly placed (e.g. genes.bed or repeats.bed).">
+		<option value="none" selected="true">None</option>
+		<option value="include">within specified regions</option>
+		<option value="exclude">outside specified regions</option>
+	    </param>
+	    <when value="include">
+		    <param name="limitfile" type="data" format="interval" label="specify regions"/>
+	    </when>
+	    <when value="exclude">
+		    <param name="limitfile" type="data" format="interval" label="specify regions"/>
+	    </when>
+    </conditional>         
+  </inputs>
+  <outputs>
+    <data format="input" name="outfile" />
+  </outputs>
+  <help>
+  
+.. class:: infomark
+
+Every chromosome are choosed with equal probability, regardless their size. Please use the tool 'random intervals' instead for general randomization.
+
+  </help>
+</tool>