Mercurial > repos > workflow4metabolomics > ms2snoop

annotate MS2snoop.xml @ 2:a35fde23940e draft

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planemo upload commit 7bb8dbe0a0bb34d897daf11c5dd3a92e89c23944
author workflow4metabolomics
date Wed, 08 Jun 2022 12:37:53 +0000
parents df2672c37732
children c68c94865667
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1 <tool id="ms2snoop" name="MS2 Snoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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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>
2
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5 <macros>
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6 <token name="@TOOL_VERSION@">1.0.1</token>
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7 <token name="@VERSION_SUFFIX@">1</token>
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8 </macros>
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>
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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 '$__tool_directory__/MS2snoop.R' --version | head -n 1
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31 </version_command>
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32 <command>
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33 <![CDATA[
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34 Rscript '$__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>
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49 <inputs>
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50 <param
2
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51 argument="--compound_txt"
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52 type="data"
1
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53 format="tabular,csv"
2
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54 label="list of compounds"
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55 help="The table must fit the format: col1=Name of molecule, col2=m/z, col3=retention time"
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56 />
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57 <param
2
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58 argument="--peaklist_frag_tsv"
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59 type="data"
1
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60 format="tabular,csv"
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61 label="MSpurity fragments file"
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62 />
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63 <param
2
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64 argument="--peaklist_preco_tsv"
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65 type="data"
1
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66 format="tabular,csv"
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67 label="MSpurity precursors file"
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68 />
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69 <param
2
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70 argument="--tolmz"
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71 type="float"
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72 min="0.0001"
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73 max="10"
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74 value="0.01"
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75 label="MZ Tolerence"
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76 />
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77 <param
2
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78 argument="--tolrt"
0
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79 type="integer"
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80 min="0"
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81 max="30"
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82 value="20"
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83 label="RT Tolerence"
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84 />
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85 <param
2
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86 argument="--seuil_ra"
0
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87 type="float"
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88 min="0"
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89 max="1"
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90 value="0.05"
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91 label="r pearson correlation threshold between precursor and fragment absolute intensity"
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92 />
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93 <param
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94 argument="--mzdecimal"
0
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95 type="integer"
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96 min="0"
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97 max="5"
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98 value="0"
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99 label="nb decimal for mz"
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100 />
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101 <param
2
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102 argument="--r_threshold"
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103 type="float"
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104 min="0"
1
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105 value="0.85"
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106 label="fragment absolute intensity"
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107 />
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108 <param
2
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109 argument="--min_number_scan"
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110 type="integer"
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111 min="0"
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112 max="25"
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113 value="8"
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114 label="Present in at least X scan"
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115 help="fragments are kept if they are found in a minimum number of scans"
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116 />
1
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117 <section title="Advenced Options" name="advenced">
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118 <param
2
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119 argument="--verbose"
1
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120 type="boolean"
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121 value=""
2
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122 optional="true"
1
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123 label="Verbose logs"
2
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124 help="The tool will print more logs"
1
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125 truevalue="--verbose"
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126 falsevalue=""
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127 />
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128 <param
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129 argument="--debug"
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130 type="boolean"
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131 value=""
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132 optional="true"
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133 label="Debug statements"
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134 help="The tool will print debug statements"
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135 truevalue="--debug"
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136 falsevalue=""
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137 />
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138 </section>
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139 </inputs>
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140 <outputs>
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141 <data
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142 name="frag_result_txt"
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143 format="tabular"
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144 label="compound_fragments_result.txt"
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145 />
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146 </outputs>
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147 <tests>
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148 <test>
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149 <param name="compound_txt" value="compounds_pos.txt" />
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150 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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151 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
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152 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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153 </test>
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154 </tests>
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155 <help><![CDATA[
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156 .. class:: infomark
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157
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158 **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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159
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160 .. class:: infomark
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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 ==============
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166 MS2 validation
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167 ==============
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168
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169 -----------
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170 Description
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171 -----------
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172
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173 MS2snoop use results of msPurity to find spectra of standards listed in a compounds file.
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174 Check the fragments and precursor using correlation of among the different scans of fragments
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175
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176 -----------------
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177 Workflow position
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178 -----------------
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179
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180 --------------
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181 Upstream tools
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182 --------------
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183
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184 +-------------------------+-----------------+--------+------------+
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185 | Name | output file | format | parameter |
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186 +=========================+=================+========+============+
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187 | msPurity.purityA | NA | TSV | NA |
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188 +-------------------------+-----------------+--------+------------+
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189 | msPurity.frag4feature | NA | TSV | NA |
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190 +-------------------------+-----------------+--------+------------+
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191
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192 ----------------
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193 Downstream tools
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194 ----------------
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195
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196 +-------------------------+-----------------+--------+------------+
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197 | Name | output file | format | parameter |
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198 +=========================+=================+========+============+
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199 | NA | NA | NA | NA |
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200 +-------------------------+-----------------+--------+------------+
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201
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202
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203 -----------
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204 Input files
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205 -----------
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206
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207 +----------------------------------------------+------------+
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208 | Parameter : num + label | Format |
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209 +===========================+==================+============+
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210 | Input from msPurity Precursor | TSV |
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211 +----------------------------------------------+------------+
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212 | Input from msPurity fragment | TSV |
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213 | Input compounds file to search in precursor | |
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214 +----------------------------------------------+------------+
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215 | and fragment (Name + m/z + ret Time) | TSV |
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216 +----------------------------------------------+------------+
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217
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218
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219 ----------
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220 Parameters
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221 ----------
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222
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223 msPurity.purityA
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224 | output TSV file
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225
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226 msPurity.frag4feature
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227 | output TSV file
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228
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229 Compounds file
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230 | A TSV TXT file with a list of compounds with at least 3 columns :
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231 | col1=Name of molecule, col2=m/z, col3=retention time
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232
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233 tolerance for mz(dalton) rt(seconds) to match the standard in the compounds file with the precursor MSpurity files
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234 | tolmz <- 0.01
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235 | tolrt <- 20
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236
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237 relative intensity threshold
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238 | seuil_ra = 0.05
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239
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240 nb decimal for mz
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241 | mzdecimal <- 0
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242
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243 r pearson correlation threshold between precursor and fragment absolute intensity
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244 | r_threshold <- 0.85
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245
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246 fragments are kept if there are found in a minimum number of scans
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247 | minNumberScan <- 8
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248
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249 ------------
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250 Output files
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251 ------------
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252
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253 compound_fragments_result.tsv
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254 | tabular output
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255 | Array with p rows (corresponding to the fragments for the different compounds of the compounds file)
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256 | Last column "corvalid" is a boolean for validated fragments
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257
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258 processing_file.pdf
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259 | pdf output
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workflow4metabolomics
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260 | 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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91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
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261 ]]></help>
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
workflow4metabolomics
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262 </tool>