# HG changeset patch
# User lain
# Date 1650458463 0
# Node ID c94a5822d31562f118496f5f94489627bb7aac30
# Parent  e1c0f63872c4f35843b64fdad0ca85b8a142eef5
" master branch Updating"

diff -r e1c0f63872c4 -r c94a5822d315 MS2snoop.xml
--- a/MS2snoop.xml	Tue Apr 19 10:21:42 2022 +0000
+++ b/MS2snoop.xml	Wed Apr 20 12:41:03 2022 +0000
@@ -53,4 +53,90 @@
             <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>