Mercurial > repos > xuebing > bed_to_bigwig

changeset 0:abb55c0cfe38

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Uploaded
author xuebing
date Sat, 31 Mar 2012 14:03:46 -0400
parents
children ccd3fd69df1a
files bed_to_bigwig.xml
diffstat 1 files changed, 37 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bed_to_bigwig.xml	Sat Mar 31 14:03:46 2012 -0400
@@ -0,0 +1,37 @@
+<tool id="bed_to_bigwig" name="bed_to_bigwig">
+  <description>make bigwig from BED or BAM</description>
+  <command interpreter="sh"> bed_to_bigwig.sh $input $outfile 
+    #if $inputa_format.bedorbam == "bed":
+    bed
+    #else:
+    bam
+    #end if
+    $sorted $genome none $split >$log 2> $log </command>
+  <inputs>
+      <conditional name="inputa_format">
+    	<param name="bedorbam" type="select" label="Select input format" >
+		<option value="bed" selected="true">BED</option>
+		<option value="bam"> BAM</option>
+	    </param>
+	    <when value="bed">
+		    <param name="input" type="data" format="bed" label="Input file"/>
+	    </when>
+	    <when value="bam">
+		    <param name="input" type="data" format="bam" label="Input file"/>
+	    </when>
+    </conditional>
+    <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="sorted" label="Check if the input is sorted" type="boolean" truevalue="sorted" falsevalue="none" checked="False"/>
+    <param name="split" label="Split junctions" help="Treat 'split' BAM or BED12 entries as distinct BED intervals." type="boolean" truevalue="-split" falsevalue="" checked="False"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="log" label="makebigwig LOG" />
+        <data format="bigwig" name="outfile" />
+
+  </outputs>
+</tool>