computational-metabolomics / mspurity-galaxy

Galaxy tools for msPurity package: includes precursor ion purity calculations and spectral matching
GNU General Public License v3.0
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Double input support #11

Closed jsaintvanne closed 5 years ago

jsaintvanne commented 5 years ago

@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...

jsaintvanne commented 5 years ago

Can close it also @Tomnl I think :)