If a journal publishing an article about a software tool requires the software to be freely available, must the article be open access?
The two are entirely independent.

The journal does not require you to make the software open source. It merely requires you to make it free for non-commercial use for at least two full years from the day of submission of the article.
It however recommends that you make the source available, preferably via an open source license. But it states that it is even acceptable to simply provide the compiled binary to the editors. (Presumably to verify that the software does what you report it to do.)

The requirement is only applied to a software if you wish to publish a paper describing a new software tool or a new implementation or algorithm. (Which seems to be your case as you want to write about a new bioinformatics software.)

The OA publishing option is something else entirely. The default publishing format in the journal is subscriber pays. With payment of additional fees you can purchase the option to make your paper open access, but that is not a requirement.

I note that the condition described in point 1 would be evaluated at the time of submission by the editorial board, whereas the possibility of publishing the article open access will not generally be discussed at all until after the paper is accepted.