As a human using the variant traits, you gain proficiency in one skill of your choice.  Can you choose a tool or does it have to be one of the listed skills?  

Outside of the tool proficiencies granted by race, class, or background, how can you gain proficiency in a specific tool.  For example if I roll up a human acolyte of Pelor, nothing in human, cleric, or acolyte gives me tool proficiencies.  How can I make him proficient with an herbalism kit?  Could I use that "one skill of my choice" granted by the variant human traits?

Thanks!

The rules will tell you if you can choose a tool proficiency and/or a skill proficiency. Since this specific rule mentions only skills, then you can't pick a tool.

You can do a Custom Background:

You might want to tweak some of the features of a background so it better fits your character or the campaign setting. To customize a background, you can replace one feature with any other one, choose any two skills, and choose a total of two tool proficiencies or languages from the sample backgrounds. You can either use the equipment package from your background or spend coin on gear as described in the Equipment section. (If you spend coin, you can’t also take the equipment package suggested for your class.) Finally, choose two personality traits, one ideal, one bond, and one flaw. If you can’t find a feature that matches your desired background, work with your DM to create one.

DDB has this built in to the character builder, which lets you pick from an assortment of skill/tool proficiency & language choices, and then select the background feature & characteristics of the Acolyte.

Edit: More info

So in the above situation, the only way to gain proficiency with an herbalism kit would to take the Skilled feat which gives you proficiency in 3 skills or tools?

Check my comment just above yours. Customizing a background is totally rules-allowed.

Awesome!  Thanks!