I don't believe that you CAN create JavaDoc out of a Jar file.
JavaDoc Options
As parameters to JavaDoc, you can specify a single source file, multiple source files, or package names. If you specify a package name, you will get documentation for all the classes in the package, including a class hierarchy and an index. Javadoc searches your CLASSPATH for the specified files. To include directories that are not in your classpath, you can specify -classpath parameter to Javadoc to add those.
-classpath (specify the classpath to use)
-sourcepath (specify where the source files (.java) are, not the .class files.)
-version (If a version tag is found, it will be included in the documentation)
-author (If an author tag is found, it will be included in the documentation
-noindex (do not generate index)
-notree (do not generate tree information)
-d (specify the directory for the output files)
-verbose (produce a detailed listing from the JavaDoc compilation)
There is no mention in this of a source jar being an input.
However, there is nothing stopping you from decompressing the jar into a temp directory, running the utility against the source files and then deleting the temp directory. Any unzip or File Librarian type of utility will unzip them... I peek at one or two all the time.