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Update file-handling.md
anjag01 May 9, 2025
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anjag01 May 22, 2025
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17 changes: 16 additions & 1 deletion docs/getting-started/types-of-topp-tools/file-handling.md
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Expand Up @@ -33,6 +33,21 @@ The TOPP tools work only on the HUPO-PSI `mzML` format. If you need to convert *
For format names as file extension, the tool derives the format from the extension. For other extensions, the file
formats of the input and output file can be given explicitly.

## Compression of mzML files

TOPP tools now support writing compressed .mzML.gz files for efficient storage. For example, PeakPickerHiRes can output compressed files:

`PeakPickerHiRes -in input.mzML -out output.mzML.gz -threads 8`

Compression uses pigz (parallel gzip) if installed for faster performance, falling back to OpenMS's internal compression mechanism otherwise. When using pigz, OpenMS limits threads to the user-specified value (e.g., -threads 8) via omp_get_max_threads(), ensuring compatibility with cluster schedulers. Install pigz for optimal speed.

Trade-offs:

Efficiency: .mzML.gz files are 2-3x smaller; pigz is significantly faster but CPU-intensive.
Compatibility: Ensure downstream tools support .mzML.gz.

This feature supports indexed mzML and enhances data management.

## Converting between DTA and mzML

Sequest DTA files can be extracted from a mzML file using the `DTAExtractor`:
Expand Down Expand Up @@ -119,4 +134,4 @@ It can currently write the following formats:

This example shows how to convert pepXML to idXML:

`IDFileConverter -in infile.pepXML -out outfile.idXML`
`IDFileConverter -in infile.pepXML -out outfile.idXML`
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