Reviewer response for version 1
The manuscript by Turaga et al. is a useful guide for novice and advanced users of R/Bioconductor and Galaxy to incorporate any R/Bioconductor packages within the popular Galaxy software. 
We believe that by allowing users to integrate any Bioconductor package within Galaxy will add enormous utility and advancement for any analyst. 
We envision users with little experience with R/Bioconductor would eventually be able to seek support to integrate any new Bioconductor package and thus incorporate the workflow within their data analysis pipeline within Galaxy. 
The authors have done an excellent job by highlighting several key best practices to achieve a reliable integration as well as the necessary structure to integrate a new BioC packages with example files highlighted within their supplemental data. 
This integration is explained through two distinct processes; 
A manual version and a semi-automated process that utilizes the tool Planemo ( https://github.com/galaxyproject/planemo ), a command-line suite of tool to assist in developing tools for the Galaxy Project. 
The authors envision a more streamlined version of their tool with subsequent improvements, and the expectations will eventually lead to a larger base of users (little and no experience in R to advanced users).
The text is well-written and is well structured, and we were able to follow the manual integration. 
However, due in part to a non-working version of the latest build from the GitHub repository, we were unable to implement the planemo tool `bioc_tool_init` and thus we can not provide a thorough evaluation of the tool. 
We expect that once the tool is available, we can provide a proper evaluation by integrating a random BioC package.
Some minor points:
- In the tool dependency file description, we were unable to understand how and where one would obtain the name and owner of each dependency. 
For example, we were unable to find the name and owner of seqTools in https://toolshed.g2.bx.psu.edu/ .
- In the tool integration section, the code has the full path and the relative path for the file in the section. 
We feel this is redundant. 
Please consider modifying the code. 
https://gist.github.com/tiagochst/a7b0ff56a864ca1ae2d5eaeaee82db9b
- This issue is probably not the author's fault, but the supplementary files do not possess the same name as the example. 
For this reason, the user has to download and rename them to execute the guide. 
Maybe adding a compressed zip with the correct names would help.
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Major problems:
Planemo: `bioc_tool_init` unavailable
As explained in the methods section we were able to install the latest version of Planemo (0.36.1). 
However, the command `bioc_tool_init` was unavailable and thus we were unable to evaluate the command by testing it with our packages. 
We followed the following instructions posted here: https://github.com/galaxyproject/planemo (Here is a screenshot of the version and the problem we experienced during install https://goo.gl/kyh33j ). 
If further steps are required to install the `bioc_tool_init` function, we feel it should be well documented either in git or this manuscript. 
Due to its unavailability to test and confirm it's practicality, we are unable to accept this MS in its current form for publication. 
Once the tool is available, we can provide a complete evaluation.
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