Mercurial > repos > jcb-mpl > eics_compression
changeset 5:6e260ccff3d8 draft
Uploaded
author | jcb-mpl |
---|---|
date | Thu, 12 May 2022 12:12:43 +0000 |
parents | 64c2025cd389 |
children | d5bbd682ba77 |
files | eics_compression.xml |
diffstat | 1 files changed, 134 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/eics_compression.xml Thu May 12 12:12:43 2022 +0000 @@ -0,0 +1,134 @@ +<tool id="2021_05_eics_compression" name="MS-centroid -> compression" version="0.0.1"> + <description> by a factor k </description> + + + <requirements> + <requirement type="package" version="6.0.2">scilab</requirement> + </requirements> + + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + + <command> <![CDATA[ + $__root_dir__/packages/scilab-*/bin/scilab-cli -nb -quit -f ${script_file} +]]> + </command> + + + <configfiles> + <configfile name="script_file"> + <![CDATA[ exec("$__tool_directory__/src/mz_1_out_of_k.sci",-1); ... + exec("$__tool_directory__/src/mz_1_merge_by_k.sci",-1); ... + lasterror(); ... + k=${k}; ... + option=${option}; ... + load("${resbary_in}"); ... // the variable name must be resbary + if option==1 then ... + resbary_out=mz_1_out_of_k(resbary,k); ... + else ... + resbary_out=mz_1_merge_by_k(resbary,k); ... + end; ... + if ~isdef('resbary_out') then ... + disp('resbary_out is not defined'); ... + end; ... + resbary=resbary_out; ... // the variable name must be resbary + save("${resbary_out}",'resbary'); ... + if ~isempty(lasterror(%f)) then ... + write(0,lasterror()); ... + end; ]]> + </configfile> + </configfiles> + + + <inputs> + <param name="resbary_in" format="mat" type="data" label="MS-centroid" help="contains the fields .time et .mzdata" /> + <param name="k" value="1" type="integer" min="1" max="100" label="k" help="a number of RTs" /> + <param name="option" value="2" type="integer" min="1" max="2" label="option" help="1= 1 out of k RT; 2= mean of k RT" /> +</inputs> + + <outputs> + <data name="resbary_out" format="mat" label="MS-compressed" /> + </outputs> + + + <tests> + + <test> + <param name="resbary_in" value="VI2016_AC_4Areduit_1centroide.mat"/> + <param name="k" value="3"/> + <param name="option" value="1"/> + <output name="resbary_out" file="VI2016_AC_4Acentroide-1_k1outof3.mat" compare="sim_size" delta="1000" /> + </test> + + <test> + <param name="resbary_in" value="VI2016_AC_4Areduit_1centroide.mat"/> + <param name="k" value="3"/> + <param name="option" value="2"/> + <output name="resbary_out" file="VI2016_AC_4Acentroide-1_k_3mean.mat" compare="sim_size" delta="1000" /> + </test> + + + + </tests> + + + +<help> + + +**Authors** Jean-Claude Boulet (INRAE). + + +--------------------------------------------------- + +================================= +COMPRESSION OF A CENTROID MS DATA +================================= + + +----------- +Description +----------- + +This function reduces by a factor k the number of RTs and associated mass spectra. + + +----- +Input +----- + +**centroid MS data** + +A centroid MS data, at the HDF5-scilab format. + +**k** + +The compression factor. + +**option** + +- 1: selects one out of k RTs and associated ms. + +- 2: merges by k the RTs and associated ms + + +------- +Outputs +------- + +**compressed MS data** + +A centroid MS data, similar to the input, but with k times less RTs and ms. + +</help> + + +<citations> + +</citations> + + +</tool>