MetaMorpheus to Proxl XML Converter

Use this program to convert the results of a MetaMorpheus cross-linking analysis to proxl XML suitable for import into the proxl web application.

Note: When running MetaMorpheus, you must enable output as PepXML when defining your XL Search taslk.

How To Run

1. Download the latest release.
2. Run the program java -jar metaMorph2ProxlXML.jar with no arguments to see the possible parameters.

For more information on importing data into Proxl, please see the Proxl Import Documentation.

More Information About Proxl

For more information about Proxl, visit http://proxl-ms.org/.

Command line documentation

Usage: java -jar metamorph2ProxlXML.jar -x pepXML file path -o output file path -f fasta file path -c conf file (toml file)

Options:

 -x or --pepxml       : Required. The full path to the pepXML file
 
 -o or --out-file     : Required. Full path (including file name) to which
                        to write the Proxl XML

 -c or --conf         : Required. Full path to  configuration file
                        used for the MetaMorpheus cross-linking search.
                        (e.g. XLSearchTaskconfig.toml)
                      
 -f or --fasta-file   : Required. Full path to the fasta file used in
                        the search.

Example:

java -jar metamorph2ProxlXML.jar -x ./results.pep.xml -o ./results.proxl.xml
-f /data/mass_spec/yeast.fa -c ./XLSearchTaskconfig.toml

java -jar metamorph2ProxlXML.jar -x ./results.pep.xml -o ./results.proxl.xml
-f /data/mass_spec/yeast.fa -c ./XLSearchTaskconfig.toml

java -jar metamorph2ProxlXML.jar -x .\Task1-XLSearchTask\my-edc-data.pep.XML -c ".\Task Settings\Task1-XLSearchTaskconfig.toml" -f ..\fastas\small_fasta.fasta -o my-edc-data.proxl.xml

More information: https://github.com/yeastrc/proxl-import-metamorpheus