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1 <tool id="MS2snoop" name="MS2 Snoop" version="1.0.0">
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2 <description>
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3 Extraction des spectres MS1 et adduits associées + Extraction +
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4 nettoyage automatisé des spectres MS2 Extraction des métadonnées
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5 des fichiers RAW Export en fichier idéalement en JSON
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6 </description>
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7
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8 <requirements>
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9 <requirement type="package">r-base</requirement>
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10 <requirement type="package">r-optparse</requirement>
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11 </requirements>
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12
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13 <command><![CDATA[
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14 Rscript '$__tool_directory__/MS2snoop.R'
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15 -o $frag_result_txt
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16 -c $compound_txt
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17 -f $peaklist_frag_tsv
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18 -p $peaklist_preco_tsv
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19 --tolmz $tolmz
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20 --tolrt $tolrt
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21 --seuil_ra $seuil_ra
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22 --mzdecimal $mzdecimal
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23 --r_threshold $r_threshold
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24 --min_number_scan $min_number_scan
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25 ;
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26 ]]></command>
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27
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28 <inputs>
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29 <param type="data" name="compound_txt" label="compounds_pos.txt" />
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30 <param type="data" name="peaklist_frag_tsv" label="peaklist_fragments.tsv" />
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31 <param type="data" name="peaklist_preco_tsv" label="peaklist_precursors.tsv" />
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32 <param name="tolmz" type="float" value="0.01" label="MZ Tolerence" />
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33 <param name="tolrt" type="integer" value="20" label="RT Telerence" />
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34 <param name="seuil_ra" type="float" value="0.05" label="r pearson correlation threshold between precursor and fragment absolute intensity" />
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35 <param name="mzdecimal" type="integer" value="0" label="nb decimal for mz" />
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36 <param name="r_threshold" type="float" value="0.85" label="fragment absolute intensity" />
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37 <param
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38 name="min_number_scan"
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39 type="integer"
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40 value="8"
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41 label="Present in at least X scan"
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42 help="fragments are kept if they are found in a minimum number of scans"
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43 />
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44 </inputs>
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45 <outputs>
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46 <data name="frag_result_txt" format="txt" label="compound_fragments_result.txt" />
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="compound_txt" value="compounds_pos.txt"/>
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51 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv"/>
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52 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv"/>
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53 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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54 </test>
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55 </tests>
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56 </tool>
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