--- a/MS2snoop.xml	Mon Apr 25 08:23:54 2022 +0000
+++ b/MS2snoop.xml	Tue May 24 18:14:49 2022 +0000
@@ -1,93 +1,140 @@
-<tool id="ms2snoop" name="MS2 Snoop" version="1.0.0" profile="21.05">
+<tool id="ms2snoop" name="MS2 Snoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <description>
         MS1/MS2 spectra and associated adducts extraction and cleaning
     </description>
-
+    <edam_topics>
+        <edam_topic>topic_0091</edam_topic>
+        <edam_topic>topic_3370</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_3803</edam_operation>
+        <edam_operation>operation_3860</edam_operation>
+    </edam_operations>
     <requirements>
-        <requirement type="package">r-optparse</requirement>
+        <requirement type="package" version="4.1.3">r-base</requirement>
+        <requirement type="package" version="1.7.1">r-optparse</requirement>
     </requirements>
-
-    <command><![CDATA[
+    <stdio>
+        <exit_code range="1" level="fatal" description="Missing parameter error" />
+        <exit_code range="2" level="fatal" description="Bad parameter's value" />
+        <exit_code range="3" level="fatal" description="Missing input file" />
+        <exit_code range="4:254" level="fatal" description="Unknown error" />
+        <exit_code range="255" level="fatal" description="No any result to output" />
+        <regex match="Error in\s+.*:\s+.*" />
+    </stdio>
+    <version_command>
+        Rscript '$__tool_directory__/MS2snoop.R' --version | head -n 1
+    </version_command>
+    <command>
+        <![CDATA[
 Rscript '$__tool_directory__/MS2snoop.R'
-    -o '$frag_result_txt'
-    -c '$compound_txt'
-    -f '$peaklist_frag_tsv'
-    -p '$peaklist_preco_tsv'
+    --output '$frag_result_txt'
+    --compounds '$compound_txt'
+    --fragments '$peaklist_frag_tsv'
+    --precursors '$peaklist_preco_tsv'
     --tolmz '$tolmz'
     --tolrt '$tolrt'
     --seuil_ra '$seuil_ra'
     --mzdecimal '$mzdecimal'
     --r_threshold '$r_threshold'
     --min_number_scan '$min_number_scan'
-;
-    ]]></command>
-
+    $advenced.debug
+    $advenced.verbose
+        ]]>
+    </command>
     <inputs>
         <param
             type="data"
-            format="tabular"
-            name="compound_txt"
-            label="compounds_pos.txt"
+            format="tabular,csv"
+            argument="--compound_txt"
+            label="list of compounds : col1=Name of molecule, col2=m/z, col3=retention time"
         />
         <param
             type="data"
-            format="tabular"
-            name="peaklist_frag_tsv"
-            label="peaklist_fragments.tsv"
+            format="tabular,csv"
+            argument="--peaklist_frag_tsv"
+            label="MSpurity fragments file"
         />
         <param
             type="data"
-            format="tabular"
-            name="peaklist_preco_tsv"
-            label="peaklist_precursors.tsv"
+            format="tabular,csv"
+            argument="--peaklist_preco_tsv"
+            label="MSpurity precursors file"
         />
         <param
-            name="tolmz"
             type="float"
             min="0.0001"
             max="10"
             value="0.01"
             label="MZ Tolerence"
+            argument="--tolmz"
         />
         <param
-            name="tolrt"
             type="integer"
             min="0"
             max="30"
             value="20"
             label="RT Tolerence"
+            argument="--tolrt"
         />
         <param
-            name="seuil_ra"
             type="float"
             min="0"
             max="1"
             value="0.05"
             label="r pearson correlation threshold between precursor and fragment absolute intensity"
+            argument="--seuil_ra"
         />
         <param
-            name="mzdecimal"
             type="integer"
             min="0"
             max="5"
             value="0"
             label="nb decimal for mz"
+            argument="--mzdecimal"
         />
         <param
-            name="r_threshold"
             type="float"
             min="0"
-            value="0.85" label="fragment absolute intensity"
+            value="0.85"
+            label="fragment absolute intensity"
+            argument="--r_threshold"
         />
         <param
-            name="min_number_scan"
             type="integer"
             min="0"
             max="25"
             value="8"
             label="Present in at least X scan"
+            argument="--min_number_scan"
             help="fragments are kept if they are found in a minimum number of scans"
         />
+        <section title="Advenced Options" name="advenced">
+            <param
+                type="boolean"
+                value=""
+                label="Verbose logs"
+                argument="--verbose"
+                truevalue="--verbose"
+                falsevalue=""
+                help="The tool will print more logs"
+                optional="true"
+            />
+            <param
+                type="boolean"
+                value=""
+                label="Debug statements"
+                argument="--debug"
+                truevalue="--debug"
+                falsevalue=""
+                help="The tool will print debug statements"
+                optional="true"
+            />
+        </section>
     </inputs>
     <outputs>
         <data
@@ -98,20 +145,22 @@
     </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"/>
+            <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
 
-    <help><![CDATA[
+**Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Lain Pavot (lain.pavot@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr) 
 
 .. 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  
 ==============
@@ -127,19 +176,28 @@
 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
-========================= ================= ======= =========
+--------------
+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
@@ -149,8 +207,10 @@
 | 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      |
 +----------------------------------------------+------------+
 
@@ -159,35 +219,43 @@
 Parameters
 ----------
 
-msPurity.purityA output TSV file
-msPurity.frag4feature output TSV file
+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
+  | 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
+  |   tolmz <- 0.01
+  |   tolrt <- 20
+
 relative intensity threshold
-|   seuil_ra = 0.05
+  |   seuil_ra = 0.05
+
 nb decimal for mz
-|   mzdecimal <- 0
+  |   mzdecimal <- 0
+
 r pearson correlation threshold between precursor and fragment absolute intensity
-|   r_threshold <- 0.85
+  |   r_threshold <- 0.85
+
 fragments are kept if there are found in a minimum number of scans
-|   minNumberScan <- 8
+  |   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 
+  | 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.
-
+  | 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>