Mercurial > repos > jcb-mpl > features_check_references
changeset 2:edc94aa0b5c4 draft default tip
Deleted selected files
| author | jcb-mpl |
|---|---|
| date | Thu, 12 May 2022 12:15:16 +0000 |
| parents | c1008b92a6c8 |
| children | |
| files | 2018_07_check_peaks.xml |
| diffstat | 1 files changed, 0 insertions(+), 175 deletions(-) [+] |
line wrap: on
line diff
--- a/2018_07_check_peaks.xml Thu May 12 12:15:10 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,175 +0,0 @@ -<tool id="2021_05_checks_ref_features" name="Features -> checks references" version="0.0.1"> - - <description> </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_9_compares_peaks.sci",-1); ... - lasterror(); ... - ... //load "${peaks_list}"; ... // 22avril21 - peaks_list=glx_tab2div("${peaks_list}"); ... - ... - load "${peaks_detail}"; ... - x836=glx_tab2div("${peaks_reference}"); ... - diff_mz=${diff_mz}; ... - k=${k}; ... - x_peaks_final=mz_9_compares_peaks(peaks_list,peaks_detail,x836,diff_mz,k); ... - ... - div2tab(x_peaks_final,"${x_peaks_final}"); ... - if ~isempty(lasterror(%f)); ... - write(0,lasterror()); ... - end; ]]> - </configfile> - </configfiles> - - - <inputs> - <param name="peaks_list" format="tabular" type="data" label="Features list" help="from function EIC->peaks:features" /> - <param name="peaks_detail" format="mat" type="data" label="Detailed features" help="from function EIC->peaks:features" /> - <param name="peaks_reference" format="tabular" type="data" label="Reference features" help="2columns: mz and RT, with column and line headers" /> - <param name="diff_mz" value="0.0050" type="float" label="Threshold for m/z values" /> - <param name="k" value="1" type="integer" label="Number of extracted features for each reference feature" help="the closest to the reference peak" /> - - </inputs> - - - <outputs> - <data name="x_peaks_final" format="tabular" label="Identified features" /> - </outputs> - - - <tests> - - <test> - <param name="peaks_list" value="Peaks_list.tabular"/> - <param name="peaks_detail" value="Peaks_details.mat"/> - <param name="peaks_reference" value="ref_mz_rt.tab"/> - <param name="diff_mz" value="0.0050"/> - <param name="k" value="1"/> - <output name="x_peaks_final"> - <assert_contents> - <has_text text="136.0616"/> - <has_text text="229.135"/> - </assert_contents> - </output> - </test> - - </tests> - - -<help> - - -**Author** Jean-Claude Boulet (INRA). - - ---------------------------------------------------- - -================================== -FEATURES EXPERIMENTAL VS REFERENCE -================================== - - ------------ -Description ------------ - -This function checks reference features among experimental features. - ------------ -Input files ------------ - -**Features list** - -The tabular file yielded by the function: EICs -> peaks:features - - -**Detailed features** - -The HDF5-scilab file yielded by the function: EICs -> peaks:features - - -**Reference features** - -A tabular file containing 2 columns: m/z values then retention times - -Row labels are the names of the reference features, e.g. chemical compounds - - - ----------- -Parameters ----------- - -**Threshold for m/z values** - -Observed features are associated to the reference features if 1) the difference in m/z values is under the threshold; 2) the reference RT falls within the range of the observed RTs. - -Default: 0.0050 - -**Number of extracted features for each reference feature** - -e.g. if the number is 2, the algorithm will extract the 2 experimental features closest to each reference feature. - - ------- -Output ------- - - -**Identified features** - -A tabular file with the columns: - -- name of the reference feature - -- number of the reference feature in the input file: Reference features - -- number of the experimental feature in the input files: Features List and Detailed features - -- number of identifications= the number of reference features each experimental feature has been attributed to; target = 1 - -- m/z value of the reference feature - -- m/z value of the experimental feature - -- difference of m/z values - -- RT of the reference feature - -- RT of the experimental feature - -- difference of RT - -- signal of the experimental feature - - -</help> - - -<citations> - -</citations> - - -</tool> - -