Difference between revisions of "SMRT Analyis: The input.xml file"
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| + | <div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;"> | ||
| + | /path/to/first_bax.h5 | ||
| − | + | /path/to/second_bax.h5 | |
| − | <span style="font-family:courier new,courier,monospace;"> | + | /path/to/third_bax.h5 |
| + | </div> | ||
| + | <br/>This text file is transformed to a XML file using the <span style="font-family:courier new,courier,monospace;">fofnToSmrtpipeInput.py</span> script: | ||
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| + | <div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;"> | ||
| + | module load smrtanalysis/2.3.0 | ||
| + | fofnToSmrtpipeInput.py /path/to/fofn.txt > input.xml | ||
| + | </div> | ||
| + | <br/>The resulting input.xml file: | ||
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| + | <div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;"> | ||
| + | <?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> | |
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| + | </pacbioAnalysisInputs> | ||
| + | </div> | ||
<span style="font-family:courier new,courier,monospace;"> </span> | <span style="font-family:courier new,courier,monospace;"> </span> | ||
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| + | <div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;"> | ||
| + | <?xml version="1.0"?> | ||
| − | + | <pacbioAnalysisInputs> | |
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| − | + | <dataReferences> | |
| − | + | <url ref="run:0000000-0001"><location>/path/to/bax.h5</location></url> | |
| − | + | <url ref="fastq:/path/to/Fastq"/> | |
| − | + | </dataReferences> | |
| + | </pacbioAnalysisInputs> | ||
| + | </div> | ||
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Latest revision as of 16:12, 9 March 2015
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>
