comparison freebayes-d291dc763c4c/freebayes.xml @ 2:322df5780b19 draft

Uploaded

1:5022cd74093c

<?xml version="1.0"?>
<tool id="freebayes" name="FreeBayes" version="0.9.9">
  <stdio>
   <regex match=".*" source="both" level="warning" description="freebayes said:"/>
  </stdio>
  <requirements>
    <requirement type="package" version="0.9.9_c993c5c07e7673">freebayes</requirement>
    <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <description> - Bayesian genetic variant detector</description>
  <command>
    ##set up input files

FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners.

In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development. 

Go FreeBayesMarth_ for details on FreeBayes.

or FreeBayesGit_ for source

------

If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

.. _FreeBayesMarth: http://bioinformatics.bc.edu/marthlab/FreeBayes

.. _FreeBayesGit: https://github.com/ekg/freebayes

.. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html
  </help>
</tool>

2:322df5780b19

<?xml version="1.0"?>
<tool id="freebayes" name="FreeBayes" version="8e44a20fccfe6c5c63f7e8aeb0f53548bf2e2ba7">
  <stdio>
   <regex match=".*" source="both" level="warning" description="freebayes:"/>
  </stdio>
  <requirements>
    <requirement type="package" version="8e44a20fccfe6c5c63f7e8aeb0f53548bf2e2ba7">freebayes</requirement>
    <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <description> - Bayesian genetic variant detector</description>
  <command>
    ##set up input files

FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners.

In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development. 

See FreeBayesMarth_ for details

or FreeBayesGit_ for source

------

If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

.. _FreeBayesMarth: http://bioinformatics.bc.edu/marthlab/FreeBayes

.. _FreeBayesGit: http://github.com/ekg/freebayes

  </help>
</tool>