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:
This text file is transformed to a XML file using the fofnToSmrtpipeInput.py script:
The resulting input.xml file:
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):