Mercurial > repos > jcb-mpl > features_extract
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| author | jcb-mpl |
|---|---|
| date | Thu, 12 May 2022 12:15:57 +0000 |
| parents | 247771a356a7 |
| children |
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<tool id="2021_05_features_extract" name="EICs -> Peaks:features" version="0.0.1"> <description> extracts the peaks (m/z x TR) from the EICs </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_8_peakpicking_dw.sci",-1); ... exec("$__tool_directory__/src/mz_6bis_durbin_watson.sci",-1); ... lasterror(); ... option=${option}; ... if option==1 then ... // liste ou fichier .dat load("${list_eic4_files}"); ... list_var=who_user(%f); ... n=size(list_var,1); ... for i=1:n; execstr(msprintf("type_tmp=type(%s);",list_var(i))); ... if type_tmp==15 then ... execstr(msprintf("x_tr_mz4=%s;",list_var(i))); ... break;... end; ... end; ... ... elseif option==2 then ... // tabular x_tr_mz4=glx_tab2div("${list_eic4_files}"); ... end; ... ... if isdef('x_tr_mz3'); ... x_tr_mz4=x_tr_mz3; ... end; ... ... if typeof(x_tr_mz4)=="list"; ... x_tr_mz4_i=x_tr_mz4(${no}); ... elseif typeof(x_tr_mz4)=="div"; ... x_tr_mz4_i=x_tr_mz4; ... end; ... ... [peaks_list,peaks_detail]=mz_8_peakpicking_dw(x_tr_mz4_i,[1:$],${plage_tr},${plage_min_tr},${dw_max},${signal_min},0); ... ... peaks_list.i='eic n0 '+ peaks_list.i; ... div2tab(peaks_list,"${peaks_list}"); ... // 20avril21 ... // save("${peaks_list}",'peaks_list'); ... save("${peaks_detail}",'peaks_detail'); ... ... if ~isempty(lasterror(%f)); ... write(0,lasterror()); ... end; ]]> </configfile> </configfiles> <inputs> <param name="list_eic4_files" format="mat,tabular" type="data" label="EICs files" help="a list of several files, or a single matrix EIC matrix (RT x m/z)" /> <param name="option" value="2" type="integer" min="1" max="2" label="Type of data" help="1= a list from the function: EIVs -> check reference mz; 2= an EIC matrix, e.g. from the function: EICs-synchronized -> EICs-merged" /> <param name="no" size="5" value="1" type="integer" label="Number" help="if list, from 1 to 5 " /> <param name="plage_tr" size="5" value="0.3" type="float" label="Maximum range of RT " help="in minutes" /> <param name="plage_min_tr" size="5" value="0.05" type="float" label="Minimum range of RT " help="in minutes" /> <param name="dw_max" size="5" value="1" type="float" label="Threshold for Durbin-Watson" help="a value between 0 and 2" /> <param name="signal_min" size="5" value="100000" type="float" label="Threshold for the signal max" help="peaks with signal max under this value are dropped" /> </inputs> <outputs> <data name="peaks_list" format="tabular" label="Peaks list"/> <data name="peaks_detail" format="mat" label="Peaks details" /> </outputs> <tests> <test> <param name="list_eic4_files" value="x4_list.dat"/> <param name="option" value="1"/> <param name="no" value="3"/> <param name="plage_tr" value="0.3"/> <param name="plage_min_tr" value="0.05"/> <param name="dw_max" value="1"/> <param name="signal_min" value="100000"/> <output name="peaks_list"> <assert_contents> <has_text text="0.2020"/> <has_text text="0.8740"/> <has_text text="3.2942"/> </assert_contents> </output> </test> <test> <param name="list_eic4_files" value="x4.tab"/> <param name="option" value="2"/> <param name="plage_tr" value="0.3"/> <param name="plage_min_tr" value="0.05"/> <param name="dw_max" value="1"/> <param name="signal_min" value="100000"/> <output name="peaks_list"> <assert_contents> <has_text text="0.2020"/> <has_text text="0.8740"/> <has_text text="3.2942"/> </assert_contents> </output> </test> </tests> <help> **Authors** Jean-Claude Boulet (INRA). --------------------------------------------------- ========================= PEAKS:FEATURES EXTRACTION ========================= ----------- Description ----------- A feature or peak is a signal recorded for a given m/z value and a range of retention times. This function extracts the peaks of each EIC from an EIC matrix. Note: this features extraction algorithm does not claim novelty nor higher performances. But it corresponds well to our outputs. For a basic use. ----- Input ----- **EICs files** - a matrix from e.g. the function: EICs-synchronized -> EICs-merged - or a list yielded by the function: EICs -> checks reference mz ---------- Parameters ---------- **Number** In case of a list, the number to select, from 1 to 5, corresponding to the m/z thresholds of 0.0005, 0.0010, 0.0030, 0.0050 and 0.0100 respectively **Maximum range of retention time** Default value: 0.3 **Minimum range of retention time** Default value: 0.05 **Threshold for Durbin-Watson** Default value: 1 ------- Outputs ------- **Peaks list** A file of 4 columns: RT min, RT max, m/z value and signal **Peaks detail** The file, format HDF5-scilab, contains a list. Each element of the list is associated to a peak, i.e. a line of the Peaks List output. Each element of the list contains a column vector of the signals recorded along a range of retention times, identified by the line labels. The column label is the m/z value of the peak. </help> <citations> </citations> </tool>