Mercurial > repos > jcb-mpl > ms_h5_to_dat
changeset 3:7d9779274f88 draft default tip
Deleted selected files
| author | jcb-mpl |
|---|---|
| date | Mon, 26 Apr 2021 15:51:06 +0000 |
| parents | 68f763d9dd0a |
| children | |
| files | 2018_07_mz_hdf5_to_dat.xml |
| diffstat | 1 files changed, 0 insertions(+), 114 deletions(-) [+] |
line wrap: on
line diff
--- a/2018_07_mz_hdf5_to_dat.xml Mon Apr 26 15:00:07 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,114 +0,0 @@ -<tool id="2021_05_hdf5_to_dat" name="MS .h5 -> MS .dat " version="0.0.1"> - -<description> from an Orbitrap MS </description> - - -<requirements> - <requirement type="package" >scilab</requirement> - </requirements> - - -<stdio> - <exit_code range="1:" level="fatal" /> -</stdio> - - -<command> <![CDATA[ - if [ -d $__root_dir__/packages/scilab-6.1.0 ]; then $__root_dir__/packages/scilab-6.1.0/bin/scilab-cli -nb -quit -f $* < ${script_file}; else scilab-cli -nb -quit -f $* < ${script_file}; fi -]]> -</command> - - - <configfiles> - <configfile name="script_file"> - <![CDATA[ exec("$__tool_directory__/src/mz_hdf5tosci.sci",-1); ... - if ~isdef('pls') then ... - atomsSystemUpdate(); ... - atomsInstall('FACT'); ... - atomsLoad('FACT'); ... - end; ... - lasterror(); ... - res=mz_hdf5tosci("${filein}"); ... - save("${res}",'res'); ... - if ~isempty(lasterror(%f)) then ... - write(0,lasterror()); ... - end ]]> - </configfile> - </configfiles> - - - <inputs> - <param name="filein" format="h5" type="data" label="Mass spectrum, .h5 format" /> - </inputs> - - - <outputs> - - <data name="res" format="mat" label="${filein.name}.dat" /> - - </outputs> - - - <tests> - <test> - <param name="filein" value="VI2016_AC_4Areduit_1.h5"/> - <output name="res" file="VI2016_AC_4Areduit_1.dat" compare="sim_size" delta="500" /> - </test> - </tests> - - <help> - - -**Author** Jean-Claude Boulet (INRAE). - - ---------------------------------------------------- - -================= -MS .h5 -> MS .dat -================= - ------------ -Description ------------ - -This function converts an Orbitrap HDF5 mass spectrum into a Scilab mass spectrum - ------ -Input ------ - -**an .h5 hrms** - -Previously, Orbitrap devices yielded .raw files. - -MSconvert selected MS1 and performed the conversion .raw -> .md5 - -Then HDF5View performed the conversion .md5 -> .h5 -which is the format of the input file. - - -------- -Outputs -------- - -**a .dat mass spectrum** - -This is an HDF5 file whose structure is specific to Scilab. - -It contains two fields: - -- time: the retention times, a vector; - -- mzdata: a list containing a MS1 spectrum (m/z + signals) for each retention time. - - -</help> - -<citations> - -</citations> - - - -</tool>