here are my changes for msPurity Galaxy.
I'm actually remove all indentations modifications to have less possible changes (sorry for that).
I try to explain changes file by file in lines just after :
mspurity Galaxy
On all these tools I tried to have the same plan as W4M tools. I can change it if you prefer and add it in a new commit after the PR.
lib.R
Add a lib.R file containing some repeated functions
I made this kind of file to avoid too much repeated functions in R files
@yguitton @lecorguille
here are my changes for msPurity Galaxy. I'm actually remove all indentations modifications to have less possible changes (sorry for that). I try to explain changes file by file in lines just after :
mspurity Galaxy
On all these tools I tried to have the same plan as W4M tools. I can change it if you prefer and add it in a new commit after the PR.
lib.R
Add a lib.R file containing some repeated functions I made this kind of file to avoid too much repeated functions in R files
assess_purity_msms.R
Add a log file output (not really necessary if you don't want it) Modify input of libraries Have to modify it Change names to be able to run function describe in lib.R file No need of filepaths. I retrieve it like this Other things are indentations
assess_purity_msms.xml
Add @commandRscript@ to run a R tool Change variable for inputs as singlefile_galaxyPath and singlefile_sampleName Add hidding advanced options Delete conditional for input data Add a log txt as output
create_msp.R
Adapt for W4M
create_msp.xml
Change indentation
frag4feature.R
Adapt for W4M (add log file, indentation, describe process...) Add the file matching file parameter Modify name of galaxy path and mzML files to fit with our functions getRawfilePathFromArguments and retrieveRawfileInTheWorkingDirectory. Not really need xset object keep xdata Add CSVfile verification Automatisation of convert2rawrt Suppress use_group parameter because I automated it in msPurity package Try to make an easier output table for users at the end
frag4feature.xml
Have to change version Add @command_scriptR@ Add filematchingfile parameter Try to move file load conditionnal in @command_fileload@ Add advanced hidding options (can be modify with different options easily) Add @command_logexit@ to add a log txt file Add parameter filematchingfile Add output log Modify output sqlite only when it is asking by user
macro.xml
Add @command_log_exit@ to add an exit in a log file Add @command_R_script@ to run a R tool Add @command_file_load@ to load files for tests
Here is the workflow that we thought : https://github.com/jsaintvanne/MyMSMSstudy/blob/master/MSpurity/workflow_msPurity_double_input.jpg
The 4 last files are yours that I cut at a defined RT because 2 of them were longer than others...