diff MS2snoop.xml @ 0:67733206be53 draft

" master branch Updating"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MS2snoop.xml	Thu Apr 14 10:23:15 2022 +0000
@@ -0,0 +1,56 @@
+<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>
+</tool>