diff linksBed.xml @ 0:4fb5ea02b441 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/linksBed.xml	Tue Jul 15 14:42:23 2014 -0400
@@ -0,0 +1,33 @@
+<tool id="bedtools_links" name="LinksBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        linksBed
+        -base $basename
+        -org $org
+        -db $db
+        -i $inputA
+        &gt; $output
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
+        <param name="basename" type="text" value="http://genome.ucsc.edu" label="The “basename” for the UCSC browser" />
+        <param name="org" type="text" value="human" label="The organism (e.g. mouse, human)" />
+        <param name="db" type="text" value="hg18" label="The genome build" />
+    </inputs>
+    <outputs>
+        <data name="output" format="html" />
+    </outputs>
+    <help>
+
+**What it does**
+
+Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. This is useful for cases when one wants to manually inspect through a large set of annotations or features.
+
+@REFERENCES@
+    </help>
+</tool>