Mercurial > repos > jcb-mpl > eics_check_references
changeset 2:cfcdd499c781 draft
Uploaded
author | jcb-mpl |
---|---|
date | Thu, 12 May 2022 12:11:34 +0000 |
parents | 679024760b59 |
children | b82aec727e31 |
files | eics_check_references.xml |
diffstat | 1 files changed, 154 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/eics_check_references.xml Thu May 12 12:11:34 2022 +0000 @@ -0,0 +1,154 @@ +<tool id="2021_05_eics_check_references" name="EICs -> checks reference mz" version="0.0.1"> + + <description> for 5 determined thresholds for m/z </description> + + <requirements> + <requirement type="package">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_0_publi_features4_galaxy.sci",-1); ... + exec("$__tool_directory__/src/mz_6bis_durbin_watson.sci",-1); ... + lasterror(); ... + ... + x_in=glx_tab2div("${xtrmz4}"); ... // 20avril21 + [x_bilan,x_synthese,x_tr_mz4]=mz_0_publi_features4_galaxy("${mzref}",x_in, ${electron}); ... + ... //[x_bilan,x_synthese,x_tr_mz4]=mz_0_publi_features4_galaxy("${mzref}", "${xtrmz4}", ${electron}); ... + ... + div2tab(x_bilan, "${xbilan}"); ... + save("${xsynthese}","x_synthese"); ... + save("${x_tr_mz_trouves}","x_tr_mz4"); ... + if ~isempty(lasterror(%f)); ... + write(0,lasterror()); ... + end; ]]> + </configfile> + </configfiles> + + + <inputs> + <param name="mzref" format="tabular" type="data" label="Reference m/z values" /> + <param name="xtrmz4" format="tabular" type="data" label="EICs-mean" /> + <param name="electron" size="5" value="0" type="integer" label="Electron mass" help="1=correction of the reference m/z values; 0=no correction" /> + </inputs> + + + <outputs> + <data name="xbilan" format="tabular" label="m/z check-summary" /> + <data name="xsynthese" format="mat" label="m/z check-details" /> + <data name="x_tr_mz_trouves" format="mat" label="m/z check-matrix" /> + </outputs> + + + <tests> + + <test> + <param name="mzref" value="ref_mz.tab"/> + <param name="xtrmz4" value="EICs-merged.tab"/> + <output name="xbilan"> + <assert_contents> + <has_text text="0.00034"/> + <has_text text="0.352"/> + </assert_contents> + </output> + </test> + + </tests> +<help> + + +**Author** Jean-Claude Boulet (INRA). + + +--------------------------------------------------- + +======================================================================= +CHECK REFERENCE MZ VALUES AMONG THE EICS-MEAN YIELDED BY THE PROCESSING +======================================================================= + +----------- +Description +----------- + +A matrix of EICs has been yielded by the function: MS-centroid -> EICs-individual or by the function: several EICs-shared -> one EICs-mean. + +The m/z values of these EICs are compared to reference m/z values for 5 pre-determined threshold values for m/z: 0.0005 / 0.0010 / 0.0030 / 0.0050 / 0.0100. + +This function is focused on the m/z values, it does not take into account the retention times. + + + +------ +Inputs +------ + +**reference m/z values** + +A tabular file, to the div format (first columns and rows = labels): + +- the first column corresponds to names of chemical compounds; + +- the second column contains the exact (reference) m/z values. + + +**EICs-mean or individual** + +A tabular matrix of (RT x m/z); lines are retention times and columns are EICs. + + +---------- +Parameters +---------- + +**correction of the electron mass** + +A correction can be applied to the reference m/z values. + +- 0: no correction; + +- 1: correction = subtraction of 0.00055 in the positive mode. + + + +------ +Output +------ + +**summary** + +The main results + + +**details** + +A .mat file + + +**extracted EICs** + +An EIC is associated to a reference m/z value if the absolute difference of (EIC minus reference) is under a threshold. + +Five threshold values have been pre-determined: 0.0005 / 0.0010 / 0.0030 / 0.0050 / 0.0100 + +This output contains a list of 5 data, each containing the EICs identified as reference m/z values according to a threshold. + +</help> + + +<citations> + +</citations> + + +</tool>