Mercurial > repos > jcb-mpl > features_extract
changeset 2:7e757edfa3b0 draft default tip
Deleted selected files
| author | jcb-mpl |
|---|---|
| date | Thu, 12 May 2022 12:15:57 +0000 |
| parents | 247771a356a7 |
| children | |
| files | 2018_07_extract_peaks.xml |
| diffstat | 1 files changed, 0 insertions(+), 203 deletions(-) [+] |
line wrap: on
line diff
--- a/2018_07_extract_peaks.xml Thu May 12 12:15:52 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,203 +0,0 @@ -<tool id="2021_05_extract_features" 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[ - 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_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>