diff tagBed.xml @ 6:75d323631dce draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tagBed.xml	Wed Jun 18 12:40:28 2014 -0400
@@ -0,0 +1,52 @@
+<tool id="bedtools_tagbed" name="TagBed" version="0.2.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        bedtools tag
+        -i $inputA
+        -files 
+        #for $bed in beds:
+            $bed.input
+        #end for
+        -f $overlap
+        $strand
+        -tag $tag
+        $field
+        &gt; $output
+    </command>
+    <inputs>
+        <param format="bam" name="inputA" type="data" label="BAM file"/>
+
+        <repeat name="beds" title="Add files" >
+            <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file" />
+        </repeat>
+        <expand macro="strand2" />
+        <expand macro="overlap" />
+        
+        <param name="tag" type="text" value="YB" label="Dictate what the tag should be." />
+        <param name="field" type="select" label="Use which field from the annotation files to populate tags?">
+            <option value="-labels" selected="True">labels</option>
+            <option value="-scores">Scores</option>
+            <option value="-names">Names</option>
+            <option value="-labels -intervals">Intervals</option>
+        </param>
+    </inputs>
+    </inputs>
+
+    <outputs>
+        <data format="bed" name="output" label="" />
+    </outputs>
+    <help>
+    
+**What it does**
+
+Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in an input bam file
+
+@REFERENCES@
+
+    </help>
+</tool>