diff bedtools-galaxy/genomeCoverageBed_histogram.xml @ 0:26c21c634c51

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bedtools-galaxy/genomeCoverageBed_histogram.xml	Thu Dec 29 10:20:07 2011 -0500
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+<tool id="bedtools_genomecoveragebed_histogram" name="Create a histogram of genome coverage" version="0.1.0">
+	<description>
+	</description>
+	
+	<requirements>
+        <requirement type="binary">genomeCoverageBed</requirement>
+    </requirements>
+    
+	<command>genomeCoverageBed
+        #if $input.ext == "bam"
+            -ibam '$input'
+        #else
+            -i '$input'
+            -g ${chromInfo}
+        #end if
+		#if str($max):
+          -max      $max
+        #end if
+		&gt; '$output'
+	</command>
+
+	<inputs>
+		<param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed"></param>
+		<param name="max" type="text" optional="true" label="Max depth" help="Combine all positions with a depth >= max into a single bin in the histogram."/>
+	</inputs>
+
+	<outputs>
+		<data format="tabular" name="output"  metadata_source="input" label="${input.name} (Genome Coverage Histogram)" />
+	</outputs>
+
+<help>
+**What it does**
+
+This tool calculates a histogram of genome coverage depth based on mapped reads in BAM format or intervals in BED format.
+
+
+------
+
+.. class:: warningmark
+
+This tool requires that `bedtools`__ has been installed on your system.
+
+.. class:: infomark
+
+The output file will contain five columns:
+
+    * 1. Chromosome name (or 'genome' for whole-genome coverage)
+    * 2. Coverage depth
+    * 3. The number of bases on chromosome (or genome) with depth equal to column 2.
+    * 4. The size of chromosome (or entire genome) in base pairs
+    * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2.
+
+**Example Output**::
+    
+    chr2L       0           1379895     23011544    0.0599653
+    chr2L       1           837250      23011544    0.0363839
+    chr2L       2           904442      23011544    0.0393038
+    chr2L       3           913723      23011544    0.0397072
+    chr2L       4           952166      23011544    0.0413778
+    chr2L       5           967763      23011544    0.0420555
+    chr2L       6           986331      23011544    0.0428624
+    chr2L       7           998244      23011544    0.0433801
+    chr2L       8           995791      23011544    0.0432735
+    chr2L       9           996398      23011544    0.0432999
+
+
+
+
+------
+
+This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
+
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://cphg.virginia.edu/quinlan/
+    .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
+
+
+
+</help>
+</tool>