The problems usually lie with mime type and default handlers.
Firstly, have you changed Firefox's about:config settings? ie:
network.protocol-handler.expose.magnet -> false
and reset other options
as per this Firefox deluge Q&A.
Have you set up rTorrent to watch any particular directory?
FILE: ~/.rtorrent.rc
# Maximum and minimum number of peers to connect to per torrent.
min_peers = 50
max_peers = 80
# Maximum number of simultanious uploads per torrent.
max_uploads = 5
# Global upload and download rate in KiB. "0" for unlimited.
download_rate = 0
upload_rate = 50
# Default directory to save the downloaded torrents.
directory = $HOME/torrents/downloads
# Watch a directory for new torrents
# SET your watch directory here --v
schedule = watch_directory,5,5,$HOME/torrents/watch/*.torrent
port_range = 60125-64125
port_random = yes
dht = auto
# UDP port to use for DHT.
dht_port = 63425
# Enable peer exchange (for torrents not marked private)
peer_exchange = yes
# Check hash for finished torrents.
check_hash = yes
encryption = allow_incoming,try_outgoing ,enable_retry
Then it is a simple matter of "save as" into $HOME/torrents/watch.
Change $HOME/torrents/watch to whatever torrents subfolder you use, or at least $HOME to /home/username
Create a file and add the following script:
FILE: maglink-rtorrent.sh
#!/bin/bash
cd $HOME/torrents/watch # set your watch directory here
[[ "$1" =~ xt=urn:btih:([^&/]+) ]] || exit;
echo "d10:magnet-uri${#1}:${1}e" > "meta-${BASH_REMATCH[1]}.torrent"
Don't forget to make it executable
chmod +x maglink-rtorrent.sh
This also offers the ability to download from terminal by:
cd $HOME/torrents/watch
./maglink-rtorrent.sh "MAGNET-LINK-HERE"
Further awesome Service Tips and rTorrent setup options here.
Futher credits:
Update 2:
If not using rTorrent, but kTorrent or qBittorent, then this following is the way to get that running:
# check defaults
xdg-mime query default x-scheme-handler/magnet
gvfs-mime --query x-scheme-handler/magnet
# set defaults
xdg-mime default qBittorent.desktop x-scheme-handler/magnet
gvfs-mime --set x-scheme-handler/magnet qBittorrent.desktop
There's a further setting (from memory) for whether you require commandline.
For rTorrent though, this link is the FlexGet rTorrent Magnet URI Handler
Full information here.
Hope this helps.