Mercurial > repos > iuc > bedtools
diff genomeCoverageBed_histogram.xml @ 0:b8348686a0b9 draft
Imported from capsule None
author | iuc |
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date | Tue, 04 Nov 2014 01:45:04 -0500 |
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--- /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 $max + #end if + > '$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>