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.
- Download the latest release.
- 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.
For more information about Proxl, visit http://proxl-ms.org/.
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