Mercurial > repos > workflow4metabolomics > ms2snoop

annotate MS2snoop.xml @ 0:91a3242fd67f draft

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"planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
author workflow4metabolomics
date Mon, 25 Apr 2022 08:23:54 +0000
parents
children df2672c37732
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1 <tool id="ms2snoop" name="MS2 Snoop" version="1.0.0" profile="21.05">
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2 <description>
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3 MS1/MS2 spectra and associated adducts extraction and cleaning
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4 </description>
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5
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6 <requirements>
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7 <requirement type="package">r-optparse</requirement>
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8 </requirements>
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9
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10 <command><![CDATA[
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11 Rscript '$__tool_directory__/MS2snoop.R'
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12 -o '$frag_result_txt'
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13 -c '$compound_txt'
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14 -f '$peaklist_frag_tsv'
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15 -p '$peaklist_preco_tsv'
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16 --tolmz '$tolmz'
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17 --tolrt '$tolrt'
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18 --seuil_ra '$seuil_ra'
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19 --mzdecimal '$mzdecimal'
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20 --r_threshold '$r_threshold'
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21 --min_number_scan '$min_number_scan'
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22 ;
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23 ]]></command>
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24
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25 <inputs>
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26 <param
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27 type="data"
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28 format="tabular"
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29 name="compound_txt"
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30 label="compounds_pos.txt"
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31 />
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32 <param
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33 type="data"
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34 format="tabular"
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35 name="peaklist_frag_tsv"
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36 label="peaklist_fragments.tsv"
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37 />
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38 <param
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39 type="data"
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40 format="tabular"
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41 name="peaklist_preco_tsv"
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42 label="peaklist_precursors.tsv"
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43 />
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44 <param
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45 name="tolmz"
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46 type="float"
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47 min="0.0001"
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48 max="10"
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49 value="0.01"
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50 label="MZ Tolerence"
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51 />
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52 <param
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53 name="tolrt"
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54 type="integer"
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55 min="0"
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56 max="30"
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57 value="20"
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58 label="RT Tolerence"
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59 />
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60 <param
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61 name="seuil_ra"
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62 type="float"
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63 min="0"
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64 max="1"
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65 value="0.05"
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66 label="r pearson correlation threshold between precursor and fragment absolute intensity"
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67 />
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68 <param
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69 name="mzdecimal"
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70 type="integer"
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71 min="0"
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72 max="5"
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73 value="0"
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74 label="nb decimal for mz"
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75 />
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76 <param
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77 name="r_threshold"
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78 type="float"
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79 min="0"
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80 value="0.85" label="fragment absolute intensity"
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81 />
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82 <param
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83 name="min_number_scan"
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84 type="integer"
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85 min="0"
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86 max="25"
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87 value="8"
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88 label="Present in at least X scan"
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89 help="fragments are kept if they are found in a minimum number of scans"
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90 />
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91 </inputs>
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92 <outputs>
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93 <data
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94 name="frag_result_txt"
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95 format="tabular"
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96 label="compound_fragments_result.txt"
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97 />
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98 </outputs>
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99 <tests>
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100 <test>
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101 <param name="compound_txt" value="compounds_pos.txt"/>
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102 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv"/>
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103 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv"/>
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104 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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105 </test>
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106 </tests>
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107
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108 <help><![CDATA[
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109
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110 .. class:: infomark
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111 **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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112 .. class:: infomark
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113 ---------------------------------------------------
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114
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115 ==============
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116 MS2 validation
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117 ==============
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118
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119 -----------
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120 Description
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121 -----------
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122
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123 MS2snoop use results of msPurity to find spectra of standards listed in a compounds file.
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124 Check the fragments and precursor using correlation of among the different scans of fragments
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125
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126 -----------------
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127 Workflow position
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128 -----------------
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129
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130 **Upstream tools**
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131 ========================= ================= ======= =========
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132 Name output file format parameter
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133 ========================= ================= ======= =========
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134 msPurity.purityA NA TSV NA
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135 msPurity.frag4feature NA TSV NA
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136 ========================= ================= ======= =========
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137 **Downstream tools**
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138 ========================= ================= ======= =========
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139 Name output file format parameter
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140 ========================= ================= ======= =========
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141 NA NA NA NA
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142 ========================= ================= ======= =========
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143
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144 -----------
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145 Input files
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146 -----------
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147
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148 +----------------------------------------------+------------+
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149 | Parameter : num + label | Format |
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150 +===========================+==================+============+
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151 | Input from msPurity Precursor | TSV |
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152 | Input from msPurity fragment | TSV |
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153 | Input compounds file to search in precursor | |
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154 | and fragment (Name + m/z + ret Time) | TSV |
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155 +----------------------------------------------+------------+
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156
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157
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158 ----------
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159 Parameters
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160 ----------
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161
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162 msPurity.purityA output TSV file
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163 msPurity.frag4feature output TSV file
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164 Compounds file
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165 | A TSV TXT file with a list of compounds with at least 3 columns :
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166 | col1=Name of molecule, col2=m/z, col3=retention time
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167 tolerance for mz(dalton) rt(seconds) to match the standard in the compounds file with the precursor MSpurity files
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168 | tolmz <- 0.01
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169 | tolrt <- 20
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170 relative intensity threshold
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171 | seuil_ra = 0.05
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172 nb decimal for mz
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173 | mzdecimal <- 0
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174 r pearson correlation threshold between precursor and fragment absolute intensity
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175 | r_threshold <- 0.85
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176 fragments are kept if there are found in a minimum number of scans
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177 | minNumberScan <- 8
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178
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179 ------------
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180 Output files
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181 ------------
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182
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183 compound_fragments_result.tsv
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184 | tabular output
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185 | Array with p rows (corresponding to the fragments for the different compounds of the compounds file)
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186 | Last column "corvalid" is a boolean for validated fragments
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187 processing_file.pdf
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188 | pdf output
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189 | 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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190
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191 ]]></help>
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192
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193 </tool>