Mercurial > repos > workflow4metabolomics > ms2snoop

annotate MS2snoop.xml @ 5:78d5a12406c2 draft

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planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3
author workflow4metabolomics
date Fri, 05 Aug 2022 17:25:45 +0000
parents 856001213966
children 77abacd33c31
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5
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1 <tool
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2 id="ms2snoop"
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3 name="MS2 Snoop"
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4 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
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5 profile="21.09"
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6 >
0
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7 <description>
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8 MS1/MS2 spectra and associated adducts extraction and cleaning
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9 </description>
2
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10 <macros>
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11 <import>macros.xml</import>
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12 </macros>
1
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13 <edam_topics>
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14 <edam_topic>topic_0091</edam_topic>
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15 <edam_topic>topic_3370</edam_topic>
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16 </edam_topics>
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17 <edam_operations>
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18 <edam_operation>operation_3803</edam_operation>
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19 <edam_operation>operation_3860</edam_operation>
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20 </edam_operations>
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21 <requirements>
1
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22 <requirement type="package" version="4.1.3">r-base</requirement>
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23 <requirement type="package" version="1.7.1">r-optparse</requirement>
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24 <requirement type="package" version="4.9.15">sirius-csifingerid</requirement>
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25 <requirement type="package" version="3.0">zip</requirement>
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26 </requirements>
1
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27 <stdio>
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28 <exit_code range="1" level="fatal" description="Missing parameter error" />
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29 <exit_code range="2" level="fatal" description="Bad parameter's value" />
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30 <exit_code range="3" level="fatal" description="Missing input file" />
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31 <exit_code range="4:254" level="fatal" description="Unknown error" />
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32 <exit_code range="255" level="fatal" description="No any result to output" />
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33 <regex match="Error in\s+.*:\s+.*" />
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34 </stdio>
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35 <version_command>
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36 Rscript '$__tool_directory__/MS2snoop.R' --version | head -n 1
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37 </version_command>
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38 <command>
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39 <![CDATA[
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40 Rscript '$__tool_directory__/MS2snoop.R'
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41 --output '$frag_result_txt'
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42 --compounds '$compound_txt'
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43 --fragments '$peaklist_frag_tsv'
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44 --precursors '$peaklist_preco_tsv'
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45 --tolmz '$tolmz'
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46 --tolrt '$tolrt'
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47 --seuil_ra '$seuil_ra'
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48 --mzdecimal '$mzdecimal'
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49 --r_threshold '$r_threshold'
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50 --min_number_scan '$min_number_scan'
5
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51 --ionization '$sirius.ionization'
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52 --fragment_match_delta '$sirius.fragment_match_delta'
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53 --fragment_match_delta_unit '$sirius.fragment_match_delta_unit'
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54 $advenced.pdf
1
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55 $advenced.debug
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56 $advenced.verbose
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57 ]]>
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58 </command>
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59 <inputs>
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60 <param
2
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61 argument="--compound_txt"
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62 type="data"
3
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63 format="tabular,csv,tsv"
2
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64 label="list of compounds"
5
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65 help="
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66 The table must fit the format:
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67 compound_name [MANDATORY] ;
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68 inchikey [MANDATORY] ;
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69 elemcomposition [OPTIONAL] ;
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70 mz [MANDATORY] ;
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71 rtsec [MANDATORY].
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72 "
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73 />
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74 <param
2
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75 argument="--peaklist_frag_tsv"
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76 type="data"
3
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77 format="tabular,csv,tsv"
1
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78 label="MSpurity fragments file"
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79 />
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80 <param
2
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81 argument="--peaklist_preco_tsv"
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82 type="data"
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83 format="tabular,csv,tsv"
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84 label="MSpurity precursors file"
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85 />
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86 <param
2
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87 argument="--tolmz"
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88 type="float"
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89 min="0.0001"
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90 max="10"
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91 value="0.01"
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92 label="MZ Tolerence"
5
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93 help="M/z tolerance to determine if a precursor matches a compound"
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94 />
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95 <param
2
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96 argument="--tolrt"
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97 type="integer"
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98 min="0"
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99 max="30"
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100 value="20"
5
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101 label="RT Tolerence (in seconds)"
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102 help="
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103 Retention time tolerance to determine if a
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104 precursor matches a compound
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105 "
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106 />
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107 <param
2
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108 argument="--seuil_ra"
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109 type="float"
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110 min="0"
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111 max="1"
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112 value="0.05"
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113 label="R-Pearson correlation threshold used to filter fragments"
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114 />
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115 <param
2
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116 argument="--mzdecimal"
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117 type="integer"
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118 min="0"
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119 max="5"
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120 value="0"
5
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121 label="Number of decimal to output M/z values with"
0
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122 />
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123 <param
2
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124 argument="--r_threshold"
0
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125 type="float"
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126 min="0"
1
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127 value="0.85"
5
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128 label="
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129 Minimun correlation with absolute intensity value to reach
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130 for a fragment to be considered as valid.
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131 In PDF generation, invalid fragments will be
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132 displayed in grey.
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133 "
0
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134 />
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135 <param
2
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136 argument="--min_number_scan"
0
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137 type="integer"
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138 min="0"
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139 max="25"
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140 value="8"
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141 label="Present in at least X scan"
5
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142 help="
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143 Mininum scan number in which a fragment must be found,
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144 to be kept.
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145 "
0
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146 />
5
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147
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148 <section title="Sirius Parameters" name="sirius">
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149 <param
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150 argument="--ionization"
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151 type="select"
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152 label="Which ionization"
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153 help="Select the ionization to use in sirius"
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154 optional="true"
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155 >
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156 <option value="[M+H]+" selected="true">[M+H]+</option>
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157 <option value="[M-H]-">[M-H]-</option>
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158 <option value="[M+?]+">[M+?]+</option>
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159 <option value="[M+K]+">[M+K]+</option>
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160 <option value="[M+Na]+">[M+Na]+</option>
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161 <option value="[M+H-H2O]+">[M+H-H2O]+</option>
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162 <option value="[M+H-H4O2]+">[M+H-H4O2]+</option>
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163 <option value="[M+NH4]+">[M+NH4]+</option>
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164 <option value="[M+Cl]-">[M+Cl]-</option>
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165 <option value="[M-H2O-H]-">[M-H2O-H]-</option>
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166 <option value="[M+Br]-">[M+Br]-</option>
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167 </param>
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168
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169 <param
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170 argument="--fragment_match_delta"
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171 type="float"
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172 min="0"
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173 max="25"
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174 value="10"
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175 label="Fragment match delta"
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176 help="
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177 Delta that determines if a fragment found by sirius
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178 is linked to a certain M/z value.
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179 Zero means all fragments found by sirius will be
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180 associated even when M/z difference is aberant.
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181 "
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182 />
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183 <param
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184 argument="--fragment_match_delta_unit"
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185 type="select"
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186 label="Delta unit"
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187 help="Select the unit of the fragment match delta"
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188 optional="true"
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189 >
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190 <option value="ppm" selected="true">PPM</option>
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191 <option value="mz">M/z</option>
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192 </param>
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193 </section>
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194
1
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195 <section title="Advenced Options" name="advenced">
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196 <param
5
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197 argument="--pdf"
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198 type="boolean"
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199 value=""
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200 optional="true"
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201 label="Output PDF"
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202 help="The tool will output some pdf in a zip file"
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203 truevalue="--pdf_path '$pdf_output'"
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204 falsevalue=""
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205 />
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206 <param
2
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207 argument="--verbose"
1
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208 type="boolean"
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209 value=""
2
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210 optional="true"
1
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211 label="Verbose logs"
2
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212 help="The tool will print more logs"
1
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213 truevalue="--verbose"
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214 falsevalue=""
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215 />
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216 <param
2
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217 argument="--debug"
1
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218 type="boolean"
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219 value=""
2
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220 optional="true"
1
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221 label="Debug statements"
2
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222 help="The tool will print debug statements"
1
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223 truevalue="--debug"
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224 falsevalue=""
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225 />
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226 </section>
0
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227 </inputs>
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228 <outputs>
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229 <data
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230 name="frag_result_txt"
5
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231 format="tsv"
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232 label="${tool.name} on ${peaklist_frag_tsv.name}"
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233 />
5
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234 <data
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235 name="pdf_output"
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236 format="zip"
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237 label="${tool.name} PDFs for ${peaklist_frag_tsv.name}"
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238 >
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239 <filter>advenced['pdf']</filter>
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240 </data>
0
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241 </outputs>
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242 <tests>
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243 <test>
5
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244 <!-- Regular test with no option -->
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245 <param
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246 name="compound_txt"
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247 value="compounds_pos.txt"
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248 />
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249 <param
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250 name="peaklist_frag_tsv"
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251 value="peaklist_fragments.tsv"
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252 />
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253 <param
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254 name="peaklist_preco_tsv"
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255 value="peaklist_precursors.tsv"
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256 />
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257 <output
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258 name="frag_result_txt"
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259 file="compound_fragments_result.txt"
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260 />
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261 <assert_stdout>
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262 <expand macro="has_regular_stdout"/>
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263 <expand macro="has_not_verbose_stdout"/>
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264 <expand macro="has_not_debug_stdout"/>
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265 </assert_stdout>
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266 </test>
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267
3
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268 <test>
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269 <!-- Regular files with verbose output -->
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270 <param
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271 name="compound_txt"
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272 value="compounds_pos.txt"
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273 />
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274 <param
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275 name="peaklist_frag_tsv"
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276 value="peaklist_fragments.tsv"
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277 />
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278 <param
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279 name="peaklist_preco_tsv"
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280 value="peaklist_precursors.tsv"
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281 />
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282 <param name="verbose" value="--verbose" />
5
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283 <output
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284 name="frag_result_txt"
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285 file="compound_fragments_result.txt"
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286 />
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287 <assert_stdout>
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288 <expand macro="has_regular_stdout"/>
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289 <expand macro="has_verbose_stdout"/>
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290 <expand macro="has_not_debug_stdout"/>
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291 </assert_stdout>
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292 </test>
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293
3
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294 <test>
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295 <!-- Regular test with debug outputs -->
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296 <param
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297 name="compound_txt"
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298 value="compounds_pos.txt"
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299 />
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300 <param
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301 name="peaklist_frag_tsv"
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302 value="peaklist_fragments.tsv"
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303 />
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304 <param
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305 name="peaklist_preco_tsv"
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306 value="peaklist_precursors.tsv"
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307 />
3
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308 <param name="debug" value="--debug" />
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309 <output
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310 name="frag_result_txt"
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311 file="compound_fragments_result.txt"
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312 />
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313 <assert_stdout>
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314 <expand macro="has_smol_stdout"/>
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315 <expand macro="has_debug_stdout"/>
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316 <expand macro="has_not_verbose_stdout"/>
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317 </assert_stdout>
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318 </test>
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319
3
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320 <test>
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321 <!-- Regular test with both verbose and debug outputs -->
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322 <param
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323 name="compound_txt"
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324 value="compounds_pos.txt"
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325 />
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326 <param
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327 name="peaklist_frag_tsv"
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328 value="peaklist_fragments.tsv"
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329 />
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330 <param
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331 name="peaklist_preco_tsv"
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332 value="peaklist_precursors.tsv"
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333 />
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334 <param name="debug" value="--debug" />
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335 <param name="verbose" value="--verbose" />
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336 <output
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337 name="frag_result_txt"
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338 file="compound_fragments_result.txt"
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339 />
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340 <assert_stdout>
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341 <expand macro="has_smol_stdout"/>
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342 <expand macro="has_debug_stdout"/>
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343 <expand macro="has_smol_verbose_stdout"/>
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344 </assert_stdout>
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345 </test>
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346
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347 <test>
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348 <!--
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349 This test mixes tsv, csv, and so, and ms2snoop is expected
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350 handle them like usual.
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351 -->
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352 <param
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353 name="compound_txt"
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354 value="compounds_pos.csv"
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355 />
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356 <param
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357 name="peaklist_frag_tsv"
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358 value="peaklist_fragments.tsv"
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359 />
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360 <param
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361 name="peaklist_preco_tsv"
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362 value="peaklist_precursors.csv"
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363 />
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364 <param name="verbose" value="--verbose" />
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365 <output
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366 name="frag_result_txt"
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367 file="compound_fragments_result.txt"
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368 />
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369 <assert_stdout>
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370 <expand macro="has_regular_stdout"/>
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371 <expand macro="has_verbose_stdout"/>
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372 <expand macro="has_not_debug_stdout"/>
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373 </assert_stdout>
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374 </test>
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375
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376 <test>
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377 <!--
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378 This test contains smaller datasets. This is the "regular"
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379 smol test, to prepare further smolah tests.
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380 -->
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381 <param name="ionization" value="[M+?]+" />
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382 <param name="mzdecimal" value="3" />
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383 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/>
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384 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" />
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385 <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" />
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386 <output name="frag_result_txt" file="smol/out-smol-base.tsv" />
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387 </test>
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388
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389 <test>
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390 <!--
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391 Test for pdf generation
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392 -->
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393 <param name="pdf" value="True" />
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394 <param name="ionization" value="[M+?]+" />
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395 <param name="mzdecimal" value="3" />
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396 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/>
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397 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" />
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398 <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" />
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399 <output name="frag_result_txt" file="smol/out-smol-base.tsv" />
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400 </test>
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401
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402 <test>
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403 <!--
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404 test for delta in ppm
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405 -->
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406 <param name="ionization" value="[M+?]+" />
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407 <param name="mzdecimal" value="3" />
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408 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/>
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409 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" />
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410 <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" />
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411 <param name="fragment_match_delta" value="8.542" />
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412 <output name="frag_result_txt" file="smol/out-smol-delta-8.542.tsv" />
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413 </test>
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414
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415 <test>
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416 <!--
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417 test for delta in m/z
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418 -->
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419 <param name="ionization" value="[M+?]+" />
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420 <param name="mzdecimal" value="3" />
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421 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/>
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422 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" />
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423 <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" />
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424 <param name="fragment_match_delta" value="0.05" />
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425 <param name="fragment_match_delta_unit" value="mz" />
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426 <output name="frag_result_txt" file="smol/out-smol-delta-0.05mz.tsv" />
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427 </test>
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428
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429 <!-- === expected to fail tests === -->
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430 <test expect_exit_code="2" expect_failure="true">
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431 <!--
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432 This test uses old format for molecules file.
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433 Is is expected to fail
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434 -->
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435 <param
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436 name="compound_txt"
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437 value="compounds_pos_old_format.txt"
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438 />
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439 <param
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440 name="peaklist_frag_tsv"
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441 value="peaklist_fragments.tsv"
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442 />
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443 <param
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444 name="peaklist_preco_tsv"
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445 value="peaklist_precursors.csv"
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446 />
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447 <assert_stderr>
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448 <has_line line="Error: Some columns are missing: compound_name, rtsec, inchikey" />
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449 </assert_stderr>
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450 </test>
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451
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452 </tests>
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453 <help><![CDATA[
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454
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455 @AUTHORS@
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456
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457 ==============
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458 MS2 validation
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459 ==============
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460
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461 -----------
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462 Description
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463 -----------
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464
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465 MS2snoop use results of msPurity to find spectra of standards listed in
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466 a compounds file. Check the fragments and precursor using correlation of
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467 among the different scans of fragments
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468
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469 -----------------
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470 Workflow position
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471 -----------------
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472
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473 --------------
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474 Upstream tools
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475 --------------
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476
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477 +-------------------------+-----------------+--------+------------+
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478 | Name | output file | format | parameter |
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479 +=========================+=================+========+============+
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480 | msPurity.purityA | NA | TSV | NA |
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481 +-------------------------+-----------------+--------+------------+
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482 | msPurity.frag4feature | NA | TSV | NA |
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483 +-------------------------+-----------------+--------+------------+
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484
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485 ----------------
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486 Downstream tools
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487 ----------------
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488
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489 +-------------------------+-----------------+--------+------------+
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490 | Name | output file | format | parameter |
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491 +=========================+=================+========+============+
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492 | NA | NA | NA | NA |
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493 +-------------------------+-----------------+--------+------------+
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494
0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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495
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496 -----------
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497 Input files
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498 -----------
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499
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500 +----------------------------------------------+------------+
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501 | Parameter : num + label | Format |
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502 +===========================+==================+============+
4
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503 | Input from msPurity Precursor | TSV,CSV |
1
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504 +----------------------------------------------+------------+
4
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505 | Input from msPurity fragment | TSV,CSV |
0
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506 | Input compounds file to search in precursor | |
1
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507 +----------------------------------------------+------------+
4
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508 | and fragment (Name + m/z + ret Time) | TSV,CSV |
0
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509 +----------------------------------------------+------------+
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510
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511
4
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512 @PARAMETERS@
1
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513
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514
4
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515 @OUTPUTS@
1
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516
0
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517
4
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518 @CHANGELOG@
0
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519
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520 ]]></help>
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521 </tool>