SMRT Analyis: The input.xml file

The input.xml file

In order to run the smrtpipe program, an input.xml file must be included. This XML file contains the filenames of the bas.h5/bax.h5 read files to be used by the pipeline. The fofnToSmrtpipeInput.py script, included in the smrtanalysis package, can create this XML file. It needs a file-of-filenames (fofn) file as input. The fofn file is simply a text file containing one filename per line, for instance:

/path/to/first_bax.h5

/path/to/second_bax.h5

/path/to/third_bax.h5

This text file is transformed to a XML file using the fofnToSmrtpipeInput.py script:

module load smrtanalysis/2.3.0

fofnToSmrtpipeInput.py /path/to/fofn.txt > input.xml

The resulting input.xml file:

<?xml version="1.0"?>

<pacbioAnalysisInputs>

  <dataReferences>

    <url ref="run:0000000-0000"><location>/path/to/first_bax.h5</location></url>

    <url ref="run:0000000-0001"><location>/path/to/second_bax.h5</location></url>

    <url ref="run:0000000-0002"><location>/path/to/third_bax.h5</location></url>

  </dataReferences>

</pacbioAnalysisInputs>

 

The fofnToSmrtpipeInput.py script can also specify an id, name, and comment for the smrtpipe job to be run. See fofnToSmrtpipeInput.py –h for details.

In addition to containing bas.h5/bax.h5 files, the input.xml can also specify filenames of fastq or fasta files (as the fofnToSmrtpipeInput.py script does not support this, such an input.xml must be manually created):

<?xml version="1.0"?>

<pacbioAnalysisInputs>

   <dataReferences>

       <url ref="run:0000000-0001"><location>/path/to/bax.h5</location></url>

       <url ref="fastq:/path/to/Fastq"/>

   </dataReferences>

</pacbioAnalysisInputs>