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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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3
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56
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57 <help><![CDATA[
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58
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59 .. class:: infomark
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60 **Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Lain Pavot (lain.pavot@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr)
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61 .. class:: infomark
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62 ---------------------------------------------------
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63
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64 ==============
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65 MS2 validation
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66 ==============
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67
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68 -----------
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69 Description
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70 -----------
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71
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72 MS2snoop use results of msPurity to find spectra of standards listed in a compounds file.
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73 Check the fragments and precursor using correlation of among the different scans of fragments
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74
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75 -----------------
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76 Workflow position
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77 -----------------
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78
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79 **Upstream tools**
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80 ========================= ================= ======= =========
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81 Name output file format parameter
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82 ========================= ================= ======= =========
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83 msPurity.purityA NA TSV NA
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84 msPurity.frag4feature NA TSV NA
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85 ========================= ================= ======= =========
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86 **Downstream tools**
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87 ========================= ================= ======= =========
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88 Name output file format parameter
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89 ========================= ================= ======= =========
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90 NA NA NA NA
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91 ========================= ================= ======= =========
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92
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93 -----------
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94 Input files
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95 -----------
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96
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97 +----------------------------------------------+------------+
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98 | Parameter : num + label | Format |
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99 +===========================+==================+============+
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100 | Input from msPurity Precursor | TSV |
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101 | Input from msPurity fragment | TSV |
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102 | Input compounds file to search in precursor | |
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103 | and fragment (Name + m/z + ret Time) | TSV |
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104 +----------------------------------------------+------------+
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105
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106
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107 ----------
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108 Parameters
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109 ----------
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110
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111 msPurity.purityA output TSV file
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112 msPurity.frag4feature output TSV file
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113 Compounds file
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114 | A TSV TXT file with a list of compounds with at least 3 columns :
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115 | col1=Name of molecule, col2=m/z, col3=retention time
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116 tolerance for mz(dalton) rt(seconds) to match the standard in the compounds file with the precursor MSpurity files
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117 | tolmz <- 0.01
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118 | tolrt <- 20
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119 relative intensity threshold
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120 | seuil_ra = 0.05
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121 nb decimal for mz
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122 | mzdecimal <- 0
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123 r pearson correlation threshold between precursor and fragment absolute intensity
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124 | r_threshold <- 0.85
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125 fragments are kept if there are found in a minimum number of scans
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126 | minNumberScan <- 8
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127
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128 ------------
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129 Output files
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130 ------------
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131
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132 compound_fragments_result.tsv
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133 | tabular output
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134 | Array with p rows (corresponding to the fragments for the different compounds of the compounds file)
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135 | Last column "corvalid" is a boolean for validated fragments
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136 processing_file.pdf
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137 | pdf output
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138 | 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.
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139
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140 ]]></help>
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141
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142 </tool>
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