Mercurial > repos > xuebing > sharplabtool

diff shuffleBed.xml @ 14:76e1b1b21cce default tip

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Deleted selected files
author xuebing
date Tue, 13 Mar 2012 19:05:10 -0400
parents 292186c14b08
children
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--- a/shuffleBed.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-<tool id="shufflebed" name="shuffleBed">
-  <description>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 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>
-    </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>