<tool id="MS2snoop" name="MS2 Snoop" version="1.0.0">
    <description>
        Extraction des spectres MS1 et adduits associées + Extraction + 
        nettoyage automatisé des spectres MS2 Extraction des métadonnées
        des fichiers RAW Export en fichier idéalement en JSON
    </description>

    <requirements>
        <requirement type="package">r-base</requirement>
        <requirement type="package">r-optparse</requirement>
    </requirements>

    <command><![CDATA[
Rscript '$__tool_directory__/MS2snoop.R'
    -o $frag_result_txt
    -c $compound_txt
    -f $peaklist_frag_tsv
    -p $peaklist_preco_tsv
    --tolmz $tolmz
    --tolrt $tolrt
    --seuil_ra $seuil_ra
    --mzdecimal $mzdecimal
    --r_threshold $r_threshold
    --min_number_scan $min_number_scan
;
    ]]></command>

    <inputs>
        <param type="data" name="compound_txt" label="compounds_pos.txt" />
        <param type="data" name="peaklist_frag_tsv" label="peaklist_fragments.tsv" />
        <param type="data" name="peaklist_preco_tsv" label="peaklist_precursors.tsv" />
        <param name="tolmz" type="float" value="0.01" label="MZ Tolerence" />
        <param name="tolrt" type="integer" value="20" label="RT Telerence" />
        <param name="seuil_ra" type="float" value="0.05" label="r pearson correlation threshold between precursor and fragment absolute intensity" />
        <param name="mzdecimal" type="integer" value="0" label="nb decimal for mz" />
        <param name="r_threshold" type="float" value="0.85" label="fragment absolute intensity" />
        <param
            name="min_number_scan"
            type="integer"
            value="8"
            label="Present in at least X scan"
            help="fragments are kept if they are found in a minimum number of scans"
        />
    </inputs>
    <outputs>
        <data name="frag_result_txt" format="txt" label="compound_fragments_result.txt" />
    </outputs>
    <tests>
        <test>
            <param name="compound_txt" value="compounds_pos.txt"/>
            <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv"/>
            <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv"/>
            <output name="frag_result_txt" file="compound_fragments_result.txt" />
        </test>
    </tests>

    <help><![CDATA[

.. class:: infomark
**Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Lain Pavot (lain.pavot@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr) 
.. class:: infomark
---------------------------------------------------

==============
MS2 validation  
==============

-----------
Description
-----------

MS2snoop use results of msPurity to find spectra of standards listed in a compounds file.
Check the fragments and precursor using correlation of among the different scans of fragments 

-----------------
Workflow position
-----------------

**Upstream tools**
========================= ================= ======= =========
Name                      output file       format  parameter
========================= ================= ======= =========
msPurity.purityA               NA             TSV      NA
msPurity.frag4feature          NA             TSV      NA
========================= ================= ======= =========
**Downstream tools**
========================= ================= ======= =========
Name                      output file       format  parameter
========================= ================= ======= =========
NA                        NA                NA      NA
========================= ================= ======= =========

-----------
Input files
-----------

+----------------------------------------------+------------+
| Parameter : num + label                      |   Format   |
+===========================+==================+============+
| Input from msPurity Precursor                |   TSV      |
| Input from msPurity fragment                 |   TSV      |
| Input compounds file to search in precursor  |            |
| and fragment (Name + m/z + ret Time)         |   TSV      |
+----------------------------------------------+------------+


----------
Parameters
----------

msPurity.purityA output TSV file
msPurity.frag4feature output TSV file
Compounds file
| A TSV TXT file with a list of compounds with at least 3 columns : 
|   col1=Name of molecule, col2=m/z, col3=retention time
tolerance for mz(dalton) rt(seconds) to match the standard in the compounds file with the precursor MSpurity files
|   tolmz <- 0.01
|   tolrt <- 20
relative intensity threshold
|   seuil_ra = 0.05
nb decimal for mz
|   mzdecimal <- 0
r pearson correlation threshold between precursor and fragment absolute intensity
|   r_threshold <- 0.85
fragments are kept if there are found in a minimum number of scans
|   minNumberScan <- 8

------------
Output files
------------

compound_fragments_result.tsv
| tabular output
| Array with p rows (corresponding to the fragments for the different compounds of the compounds file)
| Last column "corvalid" is a boolean for validated fragments 
processing_file.pdf
| pdf output 
| For each compound of the compounds file, Graph of the all fragments with parents (or most intense peak if parent is not detected in the fragments. At the end the pdf file a graph of the spectra with validated fragments.

   ]]></help>

</tool>