diff linksBed.xml @ 8:0d3aa592ce27 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/linksBed.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,54 @@
+<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>
+<![CDATA[
+        bedtools links
+            -base "${basename}"
+            -org "${org}"
+            -db "${db}"
+            -i "${input}"
+            > "${output}"
+]]>
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <param name="basename" type="text" value="http://genome.ucsc.edu"
+            label="The 'basename' for the UCSC genome browser" />
+        <param name="org" type="text" value="human" label="Organism name" help="e.g. mouse, human (-org)" />
+        <param name="db" type="text" value="hg19" label="The genome build" help="(-db)"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="html" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="linksBed1.bed" ftype="bed" />
+            <param name="basename" value="http://genome.ucsc.edu" />
+            <param name="org" value="" />
+            <param name="db" value="" />
+            <output name="output" file="linksBed_result1.html" lines_diff="2" ftype="html" />
+        </test>
+        <test>
+            <param name="input" value="linksBed1.bed" ftype="bed" />
+            <param name="basename" value="http://genome.ucsc.edu" />
+            <param name="org" value="mouse" />
+            <param name="db" value="mm9" />
+            <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**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>
+    <expand macro="citations" />
+</tool>