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-INTRODUCTION
-============
-
-This tool is part of the xcms/camera/XSeeker workflow, and it inserts
-between camera and XSeeker. It takes in input a rdata producd by camera,
-gather some data from mzxml original files, and create a database
-containing all these informations organized in such a way that XSeeker
-has just to display the data without manipulating them anymore, which
-makes it a lot faster and easier to use.
-
-
-PREREQUISITES
-=============
-There is not real preriquesite to understand how this tool works
-and to modify it. There is a single R script - XSeekerPreparator.R - that do
-all the work.
-
-You can make this tool work alone, but you can integrate it with galaxy.
-In this case, you need to have a galaxy instance you can configure.
-It is also recomended to have access to the datatypes definitions (in
-the python files) to make the outputs recognized by galaxy as XSeeker's
-database files.
-
-
-DESIGN
-======
-This tool is very simple and does a little number of things, so there is
-only a single file: XSeekerPreparator.R .
-There is a test/test.sh file that can be used as an example to know how
-to use this tool.
-
-You will find the galaxy patches in the galaxy/ directory. These files
-are not meant to be copy/paste-ed. The content of these files must be
-added to the existing files of your galaxy instance
-
-
-REQUIREMENT
-=====
-
- - R-4.0.0
- - optparse
- - xcms
- - blob
- - fst
- - DBModelR
- - stringr
- - optparse
- - galaxy (optional)
-
-#### R 4.0.0
- - `export R_MAJOR=4 R_VERSION=4.0.0 BUILD_TARGET_DIR=~/R/`
- - `wget https://cran.rstudio.com/src/base/R-${R_MAJOR}/R-${R_VERSION}.tar.gz`
- - `tar -xf "R-${R_VERSION}.tar.gz"`
- - `cd ./R-${R_VERSION}/`
- - `./configure --prefix="${BUILD_TARGET_DIR}" --with-readline="no" --with-x="no"`
- - `export CC="gcc -fPIC"`
- - `make`
- - `make install`
-
-#### Packages
-```bash
-~/R/bin/R -e "
-install.packages(
-    c(
-        'optparse',
-        'blob',
-        'fst',
-        'stringr',
-        'optparse',
-        'RSQLite',
-        'remotes',
-        'BiocManager'
-    ), repos='https://cloud.r-project.org'
-)" && \
-~/R/bin/R -e '
-    remotes::install_github("LainPavot/DBModelR", force=TRUE)
-' && \
-~/R/bin/R -e '
-    BiocManager::install("xcms")
-'
-```
-
-#### galaxy
-```bash
-git clone https://github.com/galaxyproject/galaxy
-```
-
-DEPLOY
-=====
-
-Install the tool in galaxy:  
-Open each file in the galaxy/ directory and copy their content to their
-respective files in your galaxy instance.  
-Copy XSeekerPreparator.R in galaxy/tool/tools/LC-MSMS/
-
-METADATA
---------
-
- - **@name**: XSeekerPreparator
- - **@version**: 1.1.2
- - **@authors**: Lain Pavot
- - **@date creation**: 15/09/2020
-
-NOTES
------
-Developed and tested using:
-
- - R 4.0.0
- - optparse 1.6.6
- - xcms 3.10.2
- - blob 1.2.1
- - fst 0.9.4
- - DBModelR
- - stringr 1.4.0
- - galaxy 21.01
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