Metadata-Version: 2.4
Name: r2g2
Version: 0.1.0
Summary: A tool to convert R scripts and packages to Galaxy wrappers
Home-page: https://github.com/BlankenbergLab/r2g2
Author: Jayadev Joshi
License: MIT
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: rpy2>=3.6.1
Requires-Dist: jinja2
Requires-Dist: requests
Requires-Dist: packaging
Dynamic: author
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: license
Dynamic: license-file
Dynamic: requires-dist
Dynamic: requires-python
Dynamic: summary

 ### Installation Instructions and Requirements
 
```
conda create  -n r2g2 conda-forge rpy2=3.6.2 r-base=4.4.3 python=3.12.11 r-r6=2.6.1 r-argparse=2.2.5
conda activate r2g2
pip install -r requirements.txt 
pip install r2g2
```


# R2-G2 Automatically Generates Galaxy tools on a per-function basis from any R Library

```
usage: r2g2-package [-h] --name NAME [--package_name PACKAGE_NAME] [--package_version PACKAGE_VERSION] [--out OUT] [--create_load_matrix_tool]
                    [--galaxy_tool_version GALAXY_TOOL_VERSION]

options:
  -h, --help            show this help message and exit
  --name NAME           Package Name
  --package_name PACKAGE_NAME
                        [Conda] Package Name
  --package_version PACKAGE_VERSION
                        [Conda] Package Version
  --out OUT             Output directory
  --create_load_matrix_tool
                        Output a tool that will create an RDS from a tabular matrix
  --galaxy_tool_version GALAXY_TOOL_VERSION
                        Additional Galaxy Tool Version
```

# R2-G2 Automatically Generates Galaxy tools on R-Script based on argument parsing

```
usage: r2g2-script [-h] [-r R_SCRIPT_NAME] [-f R_SCRIPTS] [-o OUTPUT_DIR] [-p PROFILE] [-d DESCRIPTION] [-s DEPENDENCIES] [-v TOOL_VERSION] [-c CITATION_DOI]
                   [-u USER_DEFINE_OUTPUT_PARAM] [-i USER_DEFINE_INPUT_PARAM]

options:
  -h, --help            show this help message and exit
  -r R_SCRIPT_NAME, --r_script_name R_SCRIPT_NAME
                        Provide the path of an R script...
  -f R_SCRIPTS, --r_scripts R_SCRIPTS
                        A path of a text file containing full path of R scripts.
  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
  -p PROFILE, --profile PROFILE
  -d DESCRIPTION, --description DESCRIPTION
                        tool based on R script
  -s DEPENDENCIES, --dependencies DEPENDENCIES
                        Extract dependency information..
  -v TOOL_VERSION, --tool_version TOOL_VERSION
                        Galaxy tool version..
  -c CITATION_DOI, --citation_doi CITATION_DOI
                        Comma separated Citation DOI.
  -u USER_DEFINE_OUTPUT_PARAM, --user_define_output_param USER_DEFINE_OUTPUT_PARAM
                        Rather guessing output params, user can define output params in specific format. Ex. 'name:protein,format:pdb,label:protein
                        file,from_work_directory;name:ligand,format:pdb,label:ligand file,from_work_directory'
  -i USER_DEFINE_INPUT_PARAM, --user_define_input_param USER_DEFINE_INPUT_PARAM
                        List of input parameters to be treated as data inputs, comma separated. Ex. 'input_file,reference_data'
```

### Provide Input and out parameter using the "--USER_DEFINE_OUTPUT_PARAM" and i "--USER_DEFINE_INPUT_PARAM" an example is provide bellow: 

```
r2g2-script -r ./tests/test_r_scripts/DEP_data_preprocessing.r -i 'input_dat,input_data_exp_design' --user_define_output_param 'output_argument:output_RDS_data,name:output_RDS_data,format:rds,label:Path to input proteomics data file,from_work_directory' -o out_test

```
