comparison bamCoverage.xml @ 10:a68a771625d2 draft

Uploaded

9:73761f33f198

<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0">
  <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage.</description>
  <requirements>
    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
    <requirement type="package" version="0.1">ucsc_tools</requirement>
    <requirement type="package" version="1.7.1">numpy</requirement>
    <requirement type="package" >deepTools</requirement>
  </requirements>
  <command>
  bamCoverage

  ##ToDo
  --numberOfProcessors 4

  --bam '$bamInput'
  --bamIndex ${bamInput.metadata.bam_index}
  --outFileName '$outFileName'
  --outFileFormat '$outFileFormat'

  </outputs>
  <help>

**What it does**

Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or read coverages. The way the method works is by first calculating all the number of reads (either extended to match the fragment length or not) that overlap each bin in the genome. Bins with zero counts are skipped, i.e. not added to the output file. The resulting read counts can be normalized using either a given scaling factor, the RPKM formula or to get a 1x depth of coverage (RPGC).

-----

.. class:: infomark

If you would like to give us feedback or you run into any trouble, please send an email to [e-mail]

This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.


.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de

</help>
</tool>

10:a68a771625d2

<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0">
    <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
    <expand macro="requirements" />
    <macros>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        bamCoverage

    @THREADS@

  --bam '$bamInput'
  --bamIndex ${bamInput.metadata.bam_index}
  --outFileName '$outFileName'
  --outFileFormat '$outFileFormat'

  </outputs>
  <help>

**What it does**

Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or read coverages. 
The way the method works is by first calculating all the number of reads (either extended to match the fragment length or not) 
that overlap each bin in the genome. Bins with zero counts are skipped, i.e. not added to the output file. 
The resulting read counts can be normalized using either a given scaling factor, the RPKM formula or to get a 1x depth of coverage (RPGC).


.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


**Output files**:

- coverage file either in bigWig or bedGraph format

-----

.. class:: infomark

@REFERENCES@

    </help>
</tool>