Mercurial > repos > workflow4metabolomics > ms2snoop

annotate MS2snoop.xml @ 1:df2672c37732 draft

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planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
author workflow4metabolomics
date Tue, 24 May 2022 18:14:49 +0000
parents 91a3242fd67f
children a35fde23940e
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1 <tool id="ms2snoop" name="MS2 Snoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
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2 <macros>
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3 <token name="@TOOL_VERSION@">1.0.1</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 </macros>
0
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6 <description>
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7 MS1/MS2 spectra and associated adducts extraction and cleaning
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8 </description>
1
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9 <edam_topics>
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10 <edam_topic>topic_0091</edam_topic>
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11 <edam_topic>topic_3370</edam_topic>
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12 </edam_topics>
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13 <edam_operations>
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14 <edam_operation>operation_3803</edam_operation>
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15 <edam_operation>operation_3860</edam_operation>
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16 </edam_operations>
0
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17 <requirements>
1
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18 <requirement type="package" version="4.1.3">r-base</requirement>
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19 <requirement type="package" version="1.7.1">r-optparse</requirement>
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20 </requirements>
1
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21 <stdio>
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22 <exit_code range="1" level="fatal" description="Missing parameter error" />
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23 <exit_code range="2" level="fatal" description="Bad parameter's value" />
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24 <exit_code range="3" level="fatal" description="Missing input file" />
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25 <exit_code range="4:254" level="fatal" description="Unknown error" />
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26 <exit_code range="255" level="fatal" description="No any result to output" />
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27 <regex match="Error in\s+.*:\s+.*" />
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28 </stdio>
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29 <version_command>
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30 Rscript '$__tool_directory__/MS2snoop.R' --version | head -n 1
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31 </version_command>
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32 <command>
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33 <![CDATA[
0
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34 Rscript '$__tool_directory__/MS2snoop.R'
1
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35 --output '$frag_result_txt'
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36 --compounds '$compound_txt'
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37 --fragments '$peaklist_frag_tsv'
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38 --precursors '$peaklist_preco_tsv'
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39 --tolmz '$tolmz'
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40 --tolrt '$tolrt'
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41 --seuil_ra '$seuil_ra'
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42 --mzdecimal '$mzdecimal'
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43 --r_threshold '$r_threshold'
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44 --min_number_scan '$min_number_scan'
1
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45 $advenced.debug
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46 $advenced.verbose
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47 ]]>
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48 </command>
0
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49 <inputs>
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50 <param
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51 type="data"
1
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52 format="tabular,csv"
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53 argument="--compound_txt"
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54 label="list of compounds : col1=Name of molecule, col2=m/z, col3=retention time"
0
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55 />
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56 <param
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57 type="data"
1
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58 format="tabular,csv"
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59 argument="--peaklist_frag_tsv"
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60 label="MSpurity fragments file"
0
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61 />
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62 <param
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63 type="data"
1
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64 format="tabular,csv"
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65 argument="--peaklist_preco_tsv"
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66 label="MSpurity precursors file"
0
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67 />
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68 <param
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69 type="float"
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70 min="0.0001"
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71 max="10"
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72 value="0.01"
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73 label="MZ Tolerence"
1
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74 argument="--tolmz"
0
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75 />
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76 <param
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77 type="integer"
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78 min="0"
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79 max="30"
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80 value="20"
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81 label="RT Tolerence"
1
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82 argument="--tolrt"
0
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83 />
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84 <param
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85 type="float"
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86 min="0"
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87 max="1"
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88 value="0.05"
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89 label="r pearson correlation threshold between precursor and fragment absolute intensity"
1
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90 argument="--seuil_ra"
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91 />
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92 <param
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93 type="integer"
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94 min="0"
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95 max="5"
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96 value="0"
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97 label="nb decimal for mz"
1
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98 argument="--mzdecimal"
0
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99 />
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100 <param
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101 type="float"
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102 min="0"
1
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103 value="0.85"
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104 label="fragment absolute intensity"
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105 argument="--r_threshold"
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106 />
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107 <param
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108 type="integer"
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109 min="0"
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110 max="25"
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111 value="8"
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112 label="Present in at least X scan"
1
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113 argument="--min_number_scan"
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114 help="fragments are kept if they are found in a minimum number of scans"
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115 />
1
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116 <section title="Advenced Options" name="advenced">
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117 <param
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118 type="boolean"
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119 value=""
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120 label="Verbose logs"
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121 argument="--verbose"
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122 truevalue="--verbose"
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123 falsevalue=""
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124 help="The tool will print more logs"
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125 optional="true"
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126 />
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127 <param
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128 type="boolean"
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129 value=""
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130 label="Debug statements"
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131 argument="--debug"
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132 truevalue="--debug"
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133 falsevalue=""
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134 help="The tool will print debug statements"
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135 optional="true"
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136 />
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137 </section>
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138 </inputs>
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139 <outputs>
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140 <data
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141 name="frag_result_txt"
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142 format="tabular"
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143 label="compound_fragments_result.txt"
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144 />
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145 </outputs>
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146 <tests>
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147 <test>
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148 <param name="compound_txt" value="compounds_pos.txt" />
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149 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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150 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
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151 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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152 </test>
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153 </tests>
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154 <help><![CDATA[
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155 .. class:: infomark
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156
1
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157 **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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158
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159 .. class:: infomark
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160
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161 ---------------------------------------------------
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162
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163
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164 ==============
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165 MS2 validation
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166 ==============
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167
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168 -----------
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169 Description
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170 -----------
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171
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172 MS2snoop use results of msPurity to find spectra of standards listed in a compounds file.
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173 Check the fragments and precursor using correlation of among the different scans of fragments
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174
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175 -----------------
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176 Workflow position
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177 -----------------
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178
1
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179 --------------
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180 Upstream tools
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181 --------------
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182
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183 +-------------------------+-----------------+--------+------------+
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184 | Name | output file | format | parameter |
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185 +=========================+=================+========+============+
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186 | msPurity.purityA | NA | TSV | NA |
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187 +-------------------------+-----------------+--------+------------+
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188 | msPurity.frag4feature | NA | TSV | NA |
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189 +-------------------------+-----------------+--------+------------+
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190
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191 ----------------
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192 Downstream tools
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193 ----------------
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194
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195 +-------------------------+-----------------+--------+------------+
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196 | Name | output file | format | parameter |
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197 +=========================+=================+========+============+
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198 | NA | NA | NA | NA |
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199 +-------------------------+-----------------+--------+------------+
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200
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201
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202 -----------
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203 Input files
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204 -----------
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205
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206 +----------------------------------------------+------------+
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207 | Parameter : num + label | Format |
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208 +===========================+==================+============+
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209 | Input from msPurity Precursor | TSV |
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210 +----------------------------------------------+------------+
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211 | Input from msPurity fragment | TSV |
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212 | Input compounds file to search in precursor | |
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213 +----------------------------------------------+------------+
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214 | and fragment (Name + m/z + ret Time) | TSV |
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215 +----------------------------------------------+------------+
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216
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217
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218 ----------
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219 Parameters
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220 ----------
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221
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222 msPurity.purityA
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223 | output TSV file
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224
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225 msPurity.frag4feature
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226 | output TSV file
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227
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228 Compounds file
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229 | A TSV TXT file with a list of compounds with at least 3 columns :
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230 | col1=Name of molecule, col2=m/z, col3=retention time
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231
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232 tolerance for mz(dalton) rt(seconds) to match the standard in the compounds file with the precursor MSpurity files
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233 | tolmz <- 0.01
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234 | tolrt <- 20
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235
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236 relative intensity threshold
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237 | seuil_ra = 0.05
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238
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239 nb decimal for mz
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240 | mzdecimal <- 0
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241
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242 r pearson correlation threshold between precursor and fragment absolute intensity
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243 | r_threshold <- 0.85
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244
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245 fragments are kept if there are found in a minimum number of scans
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246 | minNumberScan <- 8
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247
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248 ------------
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249 Output files
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250 ------------
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251
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252 compound_fragments_result.tsv
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253 | tabular output
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254 | Array with p rows (corresponding to the fragments for the different compounds of the compounds file)
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255 | Last column "corvalid" is a boolean for validated fragments
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256
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257 processing_file.pdf
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258 | pdf output
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259 | 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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260 ]]></help>
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261 </tool>