changeset 5:804fbeaa8419

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bedtools-galaxy/bamToBed.xml	Wed Dec 07 13:38:11 2011 -0500
@@ -0,0 +1,75 @@
+<tool id="bedtools_bamtobed" name="Convert from BAM to BED." version="2.14.4">
+<description></description>
+
+<requirements>
+    <requirement type="binary">bamToBed</requirement>
+</requirements>
+
+<command>
+    bamToBed $option $ed_score -i '$input' &gt; '$output' 
+    #if str($tag):
+      -tag      $tag
+    #end if
+</command>
+
+<inputs>
+    <param format="bam" name="input" type="data" label="Input BAM file"/>
+    <param name="option" type="select" label="Output formatting options">
+        <option value="">Create a 6-column BED file.</option>
+        <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
+        <option value="-bedpe">Create a paired-end, BEDPE format.</option>
+    </param>
+    <param name="split" type="boolean" label="Report spliced BAM alignments as separate BED entries." truevalue="-split" falsevalue="" checked="false"/>
+    <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/>
+    <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/>
+</inputs>
+
+<outputs>
+    <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
+</outputs>
+
+<help>
+
+**What it does**
+
+This tool converts a BAM file to a BED file. The end coordinate is computed
+by inspecting the CIGAR string. The QNAME for the alignment is used as the 
+BED name field and, by default, the MAPQ is used as the BED score.
+
+-------
+
+**Options**::
+    
+    -bedpe  Write BEDPE format.
+            - Requires BAM to be grouped or sorted by query.
+    
+    -bed12  Write "blocked" BED format (aka "BED12").
+            http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1
+    
+    -split  Report "split" BAM alignments as separate BED entries.
+    
+    -ed     Use BAM edit distance (NM tag) for BED score.
+              * Default for BED is to use mapping quality.
+              * Default for BEDPE is to use the minimum of the two mapping qualities for the pair.
+              * When -ed is used with -bedpe, the total edit distance from the two mates is reported.
+    
+    -tag    Use other NUMERIC BAM alignment tag for BED score.
+              * Default for BED is to use mapping quality.
+              * Disallowed with BEDPE output.
+<!--    
+    -color  An R,G,B string for the color used with BED12 format.
+            Default is (255,0,0).
+    
+    -cigar  Add the CIGAR string to the BED entry as a 7th column.
+-->
+
+------
+
+
+This tool is part of the `BEDTools package`__ from the `Quinlan laboratory`__.
+
+.. __: http://code.google.com/p/bedtools/
+.. __: http://cphg.virginia.edu/quinlan/
+
+</help>
+</tool>