Public bug reported:

pdfshuffler will not appear in the right-click Open With... dialog. To
fix this problem, locate the .desktop file in /usr/share/applications,
edit it as root, and add %U to the end of the Exec= line. For example,
pdfshuffler currently has this problem; you need to edit
/usr/share/applications/pdfshuffler.desktop and change the line reading
Exec=pdfshuffler to read Exec=pdfshuffler %U.

Mime type is missing as well. Just add the line
MimeType=application/pdf;

Finally the  new pdfshuffler.desktop

[Desktop Entry]
Version=1.0
Name=PDF-Shuffler
Comment=PDF Merging, Rearranging, Splitting, Rotating and Cropping
Type=Application
Exec=pdfshuffler %U
Icon=/usr/share/pdfshuffler/icons/hicolor/scalable/pdfshuffler.svg
Categories=Office;
MimeType=application/pdf;
Terminal=false
StartupNotify=false

** Affects: pdfshuffler (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: pdfshuffler

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https://bugs.launchpad.net/bugs/1349140

Title:
  pdfshuffler doesn't appear in the right click open with context menu

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