diff genomeCoverageBed_histogram.xml @ 0:b8348686a0b9 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/genomeCoverageBed_histogram.xml	Tue Nov 04 01:45:04 2014 -0500
@@ -0,0 +1,68 @@
+<tool id="bedtools_genomecoveragebed_histogram" name="Create a histogram of genome coverage" version="@WRAPPER_VERSION@.0">
+    <description>
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <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:: 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
+
+
+@REFERENCES@
+    </help>
+    <expand macro="citations" />
+</tool>