Mercurial > repos > workflow4metabolomics > ms2snoop

annotate MS2snoop.xml @ 3:c68c94865667 draft

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planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
author workflow4metabolomics
date Wed, 22 Jun 2022 13:07:01 +0000
parents a35fde23940e
children 856001213966
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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>
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5 <macros>
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6 <import>macros.xml</import>
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7 <token name="@TOOL_VERSION@">1.1.0</token>
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8 <token name="@VERSION_SUFFIX@">0</token>
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9 </macros>
1
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10 <edam_topics>
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11 <edam_topic>topic_0091</edam_topic>
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12 <edam_topic>topic_3370</edam_topic>
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13 </edam_topics>
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14 <edam_operations>
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15 <edam_operation>operation_3803</edam_operation>
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16 <edam_operation>operation_3860</edam_operation>
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17 </edam_operations>
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18 <requirements>
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19 <requirement type="package" version="4.1.3">r-base</requirement>
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20 <requirement type="package" version="1.7.1">r-optparse</requirement>
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21 </requirements>
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22 <stdio>
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23 <exit_code range="1" level="fatal" description="Missing parameter error" />
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24 <exit_code range="2" level="fatal" description="Bad parameter's value" />
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25 <exit_code range="3" level="fatal" description="Missing input file" />
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26 <exit_code range="4:254" level="fatal" description="Unknown error" />
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27 <exit_code range="255" level="fatal" description="No any result to output" />
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28 <regex match="Error in\s+.*:\s+.*" />
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29 </stdio>
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30 <version_command>
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31 Rscript '$__tool_directory__/MS2snoop.R' --version | head -n 1
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32 </version_command>
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33 <command>
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34 <![CDATA[
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35 Rscript '$__tool_directory__/MS2snoop.R'
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36 --output '$frag_result_txt'
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37 --compounds '$compound_txt'
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38 --fragments '$peaklist_frag_tsv'
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39 --precursors '$peaklist_preco_tsv'
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40 --tolmz '$tolmz'
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41 --tolrt '$tolrt'
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42 --seuil_ra '$seuil_ra'
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43 --mzdecimal '$mzdecimal'
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44 --r_threshold '$r_threshold'
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45 --min_number_scan '$min_number_scan'
1
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46 $advenced.debug
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47 $advenced.verbose
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48 ]]>
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49 </command>
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50 <inputs>
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51 <param
2
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52 argument="--compound_txt"
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53 type="data"
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54 format="tabular,csv,tsv"
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55 label="list of compounds"
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56 help="The table must fit the format: col1=Name of molecule, col2=m/z, col3=retention time"
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57 />
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58 <param
2
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59 argument="--peaklist_frag_tsv"
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60 type="data"
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61 format="tabular,csv,tsv"
1
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62 label="MSpurity fragments file"
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63 />
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64 <param
2
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65 argument="--peaklist_preco_tsv"
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66 type="data"
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67 format="tabular,csv,tsv"
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68 label="MSpurity precursors file"
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69 />
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70 <param
2
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71 argument="--tolmz"
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72 type="float"
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73 min="0.0001"
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74 max="10"
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75 value="0.01"
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76 label="MZ Tolerence"
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77 />
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78 <param
2
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79 argument="--tolrt"
0
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80 type="integer"
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81 min="0"
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82 max="30"
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83 value="20"
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84 label="RT Tolerence"
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85 />
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86 <param
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87 argument="--seuil_ra"
0
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88 type="float"
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89 min="0"
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90 max="1"
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91 value="0.05"
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92 label="r pearson correlation threshold between precursor and fragment absolute intensity"
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93 />
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94 <param
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95 argument="--mzdecimal"
0
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96 type="integer"
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97 min="0"
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98 max="5"
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99 value="0"
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100 label="nb decimal for mz"
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101 />
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102 <param
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103 argument="--r_threshold"
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104 type="float"
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105 min="0"
1
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106 value="0.85"
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107 label="fragment absolute intensity"
0
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108 />
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109 <param
2
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110 argument="--min_number_scan"
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111 type="integer"
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112 min="0"
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113 max="25"
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114 value="8"
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115 label="Present in at least X scan"
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116 help="fragments are kept if they are found in a minimum number of scans"
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117 />
1
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118 <section title="Advenced Options" name="advenced">
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119 <param
2
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120 argument="--verbose"
1
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121 type="boolean"
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122 value=""
2
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123 optional="true"
1
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124 label="Verbose logs"
2
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125 help="The tool will print more logs"
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126 truevalue="--verbose"
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127 falsevalue=""
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128 />
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129 <param
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130 argument="--debug"
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131 type="boolean"
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132 value=""
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133 optional="true"
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134 label="Debug statements"
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135 help="The tool will print debug statements"
1
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136 truevalue="--debug"
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137 falsevalue=""
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138 />
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139 </section>
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140 </inputs>
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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141 <outputs>
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142 <data
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143 name="frag_result_txt"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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144 format="tabular"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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145 label="compound_fragments_result.txt"
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146 />
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147 </outputs>
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148 <tests>
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149 <test>
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150 <param name="compound_txt" value="compounds_pos.txt" />
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151 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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152 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
0
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153 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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154 <assert_stdout>
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155 <expand macro="has_regular_stdout"/>
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156 <expand macro="has_not_verbose_stdout"/>
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157 <expand macro="has_not_debug_stdout"/>
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158 </assert_stdout>
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159 </test>
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160 <test>
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161 <param name="compound_txt" value="compounds_pos.txt" />
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162 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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163 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
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164 <param name="verbose" value="--verbose" />
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165 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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166 <assert_stdout>
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167 <expand macro="has_regular_stdout"/>
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168 <expand macro="has_verbose_stdout"/>
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169 <expand macro="has_not_debug_stdout"/>
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170 </assert_stdout>
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171 </test>
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172 <test>
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173 <param name="compound_txt" value="compounds_pos.txt" />
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174 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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175 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
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176 <param name="debug" value="--debug" />
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177 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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178 <assert_stdout>
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179 <expand macro="has_smol_stdout"/>
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180 <expand macro="has_debug_stdout"/>
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181 <expand macro="has_not_verbose_stdout"/>
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182 </assert_stdout>
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183 </test>
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184 <test>
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185 <param name="compound_txt" value="compounds_pos.txt" />
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186 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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187 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
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188 <param name="debug" value="--debug" />
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189 <param name="verbose" value="--verbose" />
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190 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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191 <assert_stdout>
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192 <expand macro="has_smol_stdout"/>
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193 <expand macro="has_debug_stdout"/>
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194 <expand macro="has_smol_verbose_stdout"/>
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195 </assert_stdout>
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196 </test>
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197 <test>
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198 <param name="compound_txt" value="compounds_pos.csv" />
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199 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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200 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
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201 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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202 <assert_stdout>
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203 <expand macro="has_regular_stdout"/>
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204 <expand macro="has_not_verbose_stdout"/>
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205 <expand macro="has_not_debug_stdout"/>
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206 </assert_stdout>
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207 </test>
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208 <test>
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209 <param name="compound_txt" value="compounds_pos.csv" />
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210 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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211 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
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212 <param name="verbose" value="--verbose" />
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213 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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214 <assert_stdout>
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215 <expand macro="has_regular_stdout"/>
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216 <expand macro="has_verbose_stdout"/>
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217 <expand macro="has_not_debug_stdout"/>
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218 </assert_stdout>
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219 </test>
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220 <test>
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221 <param name="compound_txt" value="compounds_pos.csv" />
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222 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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223 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
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224 <param name="debug" value="--debug" />
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225 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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226 <assert_stdout>
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227 <expand macro="has_smol_stdout"/>
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228 <expand macro="has_debug_stdout"/>
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229 <expand macro="has_not_verbose_stdout"/>
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230 </assert_stdout>
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231 </test>
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232 <test>
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233 <param name="compound_txt" value="compounds_pos.csv" />
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234 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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235 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
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236 <param name="debug" value="--debug" />
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237 <param name="verbose" value="--verbose" />
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238 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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239 <assert_stdout>
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240 <expand macro="has_smol_stdout"/>
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241 <expand macro="has_debug_stdout"/>
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242 <expand macro="has_smol_verbose_stdout"/>
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243 </assert_stdout>
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244 </test>
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245 </tests>
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246 <help><![CDATA[
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247 .. class:: infomark
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248
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249 **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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250
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251 .. class:: infomark
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252
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253 ---------------------------------------------------
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254
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255
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256 ==============
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257 MS2 validation
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258 ==============
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259
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260 -----------
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261 Description
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262 -----------
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263
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264 MS2snoop use results of msPurity to find spectra of standards listed in a compounds file.
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265 Check the fragments and precursor using correlation of among the different scans of fragments
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266
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267 -----------------
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268 Workflow position
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269 -----------------
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270
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271 --------------
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272 Upstream tools
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273 --------------
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274
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275 +-------------------------+-----------------+--------+------------+
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276 | Name | output file | format | parameter |
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277 +=========================+=================+========+============+
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278 | msPurity.purityA | NA | TSV | NA |
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279 +-------------------------+-----------------+--------+------------+
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280 | msPurity.frag4feature | NA | TSV | NA |
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281 +-------------------------+-----------------+--------+------------+
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282
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283 ----------------
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284 Downstream tools
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285 ----------------
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286
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287 +-------------------------+-----------------+--------+------------+
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288 | Name | output file | format | parameter |
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289 +=========================+=================+========+============+
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290 | NA | NA | NA | NA |
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291 +-------------------------+-----------------+--------+------------+
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292
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293
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294 -----------
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295 Input files
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296 -----------
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297
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298 +----------------------------------------------+------------+
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299 | Parameter : num + label | Format |
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300 +===========================+==================+============+
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301 | Input from msPurity Precursor | TSV |
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302 +----------------------------------------------+------------+
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303 | Input from msPurity fragment | TSV |
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304 | Input compounds file to search in precursor | |
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305 +----------------------------------------------+------------+
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306 | and fragment (Name + m/z + ret Time) | TSV |
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307 +----------------------------------------------+------------+
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308
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309
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310 ----------
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311 Parameters
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312 ----------
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313
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314 msPurity.purityA
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315 | output TSV file
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316
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317 msPurity.frag4feature
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318 | output TSV file
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319
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320 Compounds file
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321 | A TSV TXT file with a list of compounds with at least 3 columns :
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322 | col1=Name of molecule, col2=m/z, col3=retention time
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323
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324 tolerance for mz(dalton) rt(seconds) to match the standard in the compounds file with the precursor MSpurity files
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325 | tolmz <- 0.01
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326 | tolrt <- 20
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327
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328 relative intensity threshold
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329 | seuil_ra = 0.05
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330
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331 nb decimal for mz
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332 | mzdecimal <- 0
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333
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334 r pearson correlation threshold between precursor and fragment absolute intensity
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335 | r_threshold <- 0.85
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336
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337 fragments are kept if there are found in a minimum number of scans
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338 | minNumberScan <- 8
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339
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340 ------------
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341 Output files
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342 ------------
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343
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344 compound_fragments_result.tsv
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345 | tabular output
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346 | Array with p rows (corresponding to the fragments for the different compounds of the compounds file)
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347 | Last column "corvalid" is a boolean for validated fragments
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348
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349 processing_file.pdf
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350 | pdf output
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351 | 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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352 ]]></help>
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353 </tool>