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changeset 2:e6502d9fe0dd draft

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Uploaded
author nikos
date Tue, 15 Jul 2014 07:18:55 -0400
parents 37da191c7760
children e8301c182e8c
files bedExtendRanges.xml
diffstat 1 files changed, 68 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bedExtendRanges.xml	Tue Jul 15 07:18:55 2014 -0400
@@ -0,0 +1,68 @@
+<tool id="bedExtendRanges" name="bedExtendRanges">
+  <description> Extend length of entries in bed 6+. </description>
+  <command> 
+	## Set genome assembly 
+
+	#set $Genome = str( $genome_cond.genome )
+	#if str( $genome_cond ) == 'OTHER':
+		#set $Genome = str( $genome_cond.genome_other )
+	#end if
+	
+	bedExtendRanges -user=genome -host=genome-mysql.cse.ucsc.edu $Genome $length $input 2> /dev/null > $output
+  </command>
+  <inputs>
+    <param name="input" type="data" format="bed" label="Input"/>
+    <conditional name="genome_cond">
+      <param name="genome" type="select" label="Genome Assembly (-g)">
+        <option value="hg19">Human (Homo sapiens): hg19</option>
+        <option value="hg18">Human (Homo sapiens): hg18</option>
+        <option value="mm10">Mouse (Mus musculus): mm10</option>
+        <option value="mm9">Mouse (Mus musculus): mm9</option>
+        <option value="ce10">C. elegans: ce10</option>
+        <option value="ce6">C. elegans: ce6</option>
+        <option value="dm3">D. melanogaster: dm3</option>
+        <option value="OTHER">Other</option>
+      </param>
+      <when value="OTHER">
+        <param name="genome_other" type="text" label="Other genome assemly"/>
+      </when>
+      <when value="hg19" type="text" />
+      <when value="hg18" type="text" />
+      <when value="mm10" type="text" />
+      <when value="mm9" type="text" />
+      <when value="ce10" type="text" />
+      <when value="ce6" type="text" />
+      <when value="dm3" type="text" />
+    </conditional>
+    <param name="length" type="integer" value="0" label="Length extension (base-pairs)" />
+
+  </inputs>
+  
+  <outputs>
+    <data format="input" name="output"/> 
+  </outputs>
+  <help>
+
+**What it does**
+
+bedExtendRanges - extend length of entries in bed 6+ data to be at least the given length,
+taking strand directionality into account.
+
+**Usage**
+
+   bedExtendRanges database length files(s)
+
+**Example**
+
+  * bedExtendRanges -user=genome -host=genome-mysql.cse.ucsc.edu hg18 250 stdin
+
+  will transform:
+    chr1 500 525 . 100 +
+    chr1 1000 1025 . 100 -
+  to:
+    chr1 500 750 . 100 +
+    chr1 775 1025 . 100 -
+
+  </help>
+</tool>
+