# isolab for Galaxy #

This is Galaxy tool for R package
[IsotopicLabelling](https://github.com/RuggeroFerrazza/IsotopicLabelling)
which analyses mass spectrometric isotopic patterns obtained following
isotopic labelling experiments. For more details, see the
[IsotopicLabelling: an R package for the analysis of MS isotopic patterns of
labelled
analytes](https://academic.oup.com/bioinformatics/article/33/2/300/2525697).

## Installation ##

- Install [Galaxy](https://github.com/galaxyproject/galaxy) under Linux.

- Install [conda](https://docs.conda.io/en/latest/miniconda.html) under
  Linux. `conda` is used to install `requirements` of this tool. 

- Use `git` to clone this tool

  ```bash
  git clone https://github.com/wanchanglin/isolab.git
  ```

- Add this tool's location into Galaxy' tool config file:
  `~/Galaxy/config/tool_conf.xml`. For example, one simplified
  `tool_conf.xml` looks like:

  ```xml
  <?xml version='1.0' encoding='utf-8'?>
  <toolbox monitor="true">
    
    <section id="getext" name="Get Data">
      <tool file="data_source/upload.xml" />
    </section>
    
    <section id="MyTools" name="My Tools">
      <tool file="/path/to/isolab/isolab.xml" />
    </section>

  </toolbox>
  ```

- The Galaxy tool uses [R](https://cran.r-project.org/) packages `optparse`,
  `WriteXLS` and `gsubfn`.  All of these packages will be installed by
  `conda` in its virtual environment. Two R packages `IsotopicLabelling` and
  `ecipes` are already included.

- Some test data are located in `test-data`.

## Notes ##

- `planemo test` compares the history results in `test-data/res` produced by
  shell scripts in `test`. (27-03-2019, Wed) 
- White spaces in `groups` input: Group factor delimiter is comma. No any
  extra white spaces are allowed otherwise an error will be encountered.
  Note that `isolab.sh` has no problem with white spaces. Probably it is
  'Cheetah' or Galaxy's text input problem. (31-05-2018, Thu) 

## Authors, contributors & contacts ##

- Wanchang Lin (wl361@cam.ac.uk), University of Cambridge 
- Julian L Griffin (jlg40@cam.ac.uk), University of Cambridge