Mercurial > repos > workflow4metabolomics > ms2snoop
annotate MS2snoop.xml @ 7:2a1f120a6874 draft default tip
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| author | workflow4metabolomics |
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| date | Tue, 10 Jan 2023 11:07:48 +0000 |
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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 </macros> |
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8 <edam_topics> |
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9 <edam_topic>topic_0091</edam_topic> |
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10 <edam_topic>topic_3370</edam_topic> |
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11 </edam_topics> |
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12 <edam_operations> |
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13 <edam_operation>operation_3803</edam_operation> |
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14 <edam_operation>operation_3860</edam_operation> |
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15 </edam_operations> |
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16 <requirements> |
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17 <requirement type="package" version="4.1.3">r-base</requirement> |
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18 <requirement type="package" version="1.7.1">r-optparse</requirement> |
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19 <requirement type="package" version="4.9.15">sirius-csifingerid</requirement> |
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20 <requirement type="package" version="3.0">zip</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 <![CDATA[ |
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32 @COMMAND_RSCRIPT@ '$__tool_directory__/MS2snoop.R' --version | head -n 1 |
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33 ]]> |
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34 </version_command> |
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35 <command> |
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36 <![CDATA[ |
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37 @COMMAND_RSCRIPT@ '$__tool_directory__/MS2snoop.R' |
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38 --output '$frag_result_txt' |
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39 --compounds '$compound_txt' |
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40 --fragments '$peaklist_frag_tsv' |
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41 --precursors '$peaklist_preco_tsv' |
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42 --tolmz '$tolmz' |
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43 --tolrt '$tolrt' |
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44 --seuil_ra '$seuil_ra' |
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45 --mzdecimal '$mzdecimal' |
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46 --r_threshold '$r_threshold' |
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47 --min_number_scan '$min_number_scan' |
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48 --ionization '$sirius.ionization' |
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49 --fragment_match_delta '$sirius.fragment_match_delta' |
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50 --fragment_match_delta_unit '$sirius.fragment_match_delta_unit' |
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51 #if $advenced.pdf: |
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52 --pdf_path './out.zip' |
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53 #end if |
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54 $advenced.debug |
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55 $advenced.verbose |
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56 #if $advenced.pdf: |
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57 && cat ./out.zip > '$pdf_output' |
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58 #end if |
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59 |
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60 ]]> |
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61 </command> |
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62 <inputs> |
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63 <param argument="--compound_txt" type="data" format="tabular,csv,tsv" |
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64 label="list of compounds" |
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65 help="The table must fit the format: compound_name, inchikey, [elemcomposition], mz, rtsec." |
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66 /> |
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67 <param argument="--peaklist_frag_tsv" type="data" format="tabular,csv,tsv" |
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68 label="MSpurity fragments file" |
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69 /> |
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70 <param argument="--peaklist_preco_tsv" type="data" format="tabular,csv,tsv" |
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71 label="MSpurity precursors file" |
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72 /> |
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73 <param argument="--tolmz" type="float" min="0.0001" max="10" value="0.01" |
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74 label="MZ Tolerence" |
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75 help="M/z tolerance to determine if a precursor matches a compound" |
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76 /> |
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77 <param argument="--tolrt" type="integer" min="0" max="30" value="20" |
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78 label="RT Tolerence (in seconds)" |
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79 help="Retention time tolerance to determine if a precursor matches a compound" |
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80 /> |
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81 <param argument="--seuil_ra" type="float" min="0" max="1" value="0.05" |
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82 label="R-Pearson correlation threshold used to filter fragments" |
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83 /> |
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84 <param argument="--mzdecimal" type="integer" min="0" max="5" value="3" |
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85 label="Number of decimal to output M/z values with" |
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86 /> |
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87 <param argument="--r_threshold" type="float" min="0" value="0.85" |
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88 label=" |
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89 Minimun correlation with absolute intensity value to reach |
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90 for a fragment to be considered as valid. |
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91 In PDF generation, invalid fragments will be |
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92 displayed in grey. |
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93 " |
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94 /> |
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95 <param argument="--min_number_scan" type="integer" min="0" max="25" value="8" |
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96 label="Present in at least X scan" |
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97 help="Mininum scan number in which a fragment must be found, to be kept." |
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98 /> |
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99 |
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100 <section title="Sirius Parameters" name="sirius"> |
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101 <param argument="--ionization" type="select" optional="true" |
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102 label="Which ionization" |
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103 help="Select the ionization to use in sirius" |
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104 > |
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105 <option value="[M+H]+" selected="true">[M+H]+</option> |
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106 <option value="[M-H]-">[M-H]-</option> |
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107 <option value="[M+?]+">[M+?]+</option> |
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108 <option value="[M+K]+">[M+K]+</option> |
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109 <option value="[M+Na]+">[M+Na]+</option> |
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110 <option value="[M+H-H2O]+">[M+H-H2O]+</option> |
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111 <option value="[M+H-H4O2]+">[M+H-H4O2]+</option> |
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112 <option value="[M+NH4]+">[M+NH4]+</option> |
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113 <option value="[M+Cl]-">[M+Cl]-</option> |
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114 <option value="[M-H2O-H]-">[M-H2O-H]-</option> |
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115 <option value="[M+Br]-">[M+Br]-</option> |
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116 </param> |
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117 |
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118 <param argument="--fragment_match_delta" type="float" min="0" max="25" value="10" |
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119 label="Fragment match delta" |
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120 help=" |
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121 Delta that determines if a fragment found by sirius |
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122 is linked to a certain M/z value. |
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123 Zero means all fragments found by sirius will be |
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124 associated even when M/z difference is aberant. |
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125 " |
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126 /> |
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127 <param argument="--fragment_match_delta_unit" type="select" optional="true" |
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128 label="Delta unit" |
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129 help="Select the unit of the fragment match delta" |
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130 > |
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131 <option value="ppm" selected="true">PPM</option> |
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132 <option value="mz">M/z</option> |
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133 </param> |
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134 </section> |
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135 |
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136 <section title="Advenced Options" name="advenced"> |
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137 <param argument="--pdf" type="boolean" value="" optional="true" |
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138 label="Output PDF" |
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139 help="The tool will output some pdf in a zip file" |
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140 /> |
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141 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" value="" optional="true" |
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142 label="Verbose logs" |
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143 help="The tool will print more logs" |
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144 /> |
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145 <param argument="--debug" type="boolean" truevalue="--debug" falsevalue="" value="" optional="true" |
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146 label="Debug statements" |
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147 help="The tool will print debug statements" |
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148 /> |
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149 </section> |
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150 </inputs> |
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151 <outputs> |
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152 <data name="frag_result_txt" format="tsv" label="${tool.name}_on_${peaklist_frag_tsv.name}" /> |
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153 <data name="pdf_output" format="zip" label="${tool.name}_PDFs_for_${peaklist_frag_tsv.name}"> |
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154 <filter>advenced['pdf']</filter> |
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155 </data> |
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156 </outputs> |
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157 <tests> |
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158 <test> |
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159 <!-- #1 Regular test with no option --> |
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160 <param name="compound_txt" value="compounds_pos.txt" /> |
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161 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> |
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162 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> |
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163 <output name="frag_result_txt" file="compound_fragments_result.txt" /> |
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164 <assert_stdout> |
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165 <expand macro="has_regular_stdout"/> |
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166 <expand macro="has_not_verbose_stdout"/> |
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167 <expand macro="has_not_debug_stdout"/> |
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168 </assert_stdout> |
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169 </test> |
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170 |
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171 <test> |
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172 <!-- #2 Regular files with verbose output --> |
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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="verbose" value="--verbose" /> |
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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_regular_stdout"/> |
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180 <expand macro="has_verbose_stdout"/> |
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181 <expand macro="has_not_debug_stdout"/> |
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182 </assert_stdout> |
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183 </test> |
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184 |
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185 <test> |
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186 <!-- #3 Regular test with debug outputs --> |
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187 <param name="compound_txt" value="compounds_pos.txt" /> |
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188 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> |
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189 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> |
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190 <param name="debug" value="--debug" /> |
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191 <output name="frag_result_txt" file="compound_fragments_result.txt" /> |
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192 <assert_stdout> |
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193 <expand macro="has_smol_stdout"/> |
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194 <expand macro="has_debug_stdout"/> |
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195 <expand macro="has_not_verbose_stdout"/> |
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196 </assert_stdout> |
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197 </test> |
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199 <test> |
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200 <!-- #4 Regular test with both verbose and debug outputs --> |
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201 <param name="compound_txt" value="compounds_pos.txt" /> |
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202 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> |
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203 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> |
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204 <param name="debug" value="--debug" /> |
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205 <param name="verbose" value="--verbose" /> |
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206 <output name="frag_result_txt" file="compound_fragments_result.txt" /> |
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207 <assert_stdout> |
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208 <expand macro="has_smol_stdout"/> |
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209 <expand macro="has_debug_stdout"/> |
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210 <expand macro="has_smol_verbose_stdout"/> |
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211 </assert_stdout> |
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212 </test> |
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214 <test> |
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215 <!-- |
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216 #5 This test mixes tsv, csv, and so, and ms2snoop is expected |
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217 handle them like usual. |
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219 <param name="compound_txt" value="compounds_pos.csv" /> |
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220 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> |
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221 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> |
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222 <param name="verbose" value="--verbose" /> |
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223 <output name="frag_result_txt" file="compound_fragments_result.txt" /> |
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224 <assert_stdout> |
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225 <expand macro="has_regular_stdout"/> |
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226 <expand macro="has_verbose_stdout"/> |
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227 <expand macro="has_not_debug_stdout"/> |
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228 </assert_stdout> |
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229 </test> |
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230 |
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231 <test> |
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232 <!-- |
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233 #6 This test contains smaller datasets. This is the "regular" |
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234 smol test, to prepare further smolah tests. |
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235 --> |
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236 <param name="ionization" value="[M+?]+" /> |
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237 <param name="mzdecimal" value="3" /> |
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238 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> |
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239 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> |
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240 <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" /> |
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241 <output name="frag_result_txt" file="smol/out-smol-base.tsv" /> |
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242 </test> |
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243 |
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244 <test> |
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245 <!-- |
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246 #7 Test for pdf generation |
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247 --> |
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248 <param name="pdf" value="True" /> |
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249 <param name="ionization" value="[M+?]+" /> |
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250 <param name="mzdecimal" value="3" /> |
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251 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> |
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252 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> |
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253 <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" /> |
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254 <output name="frag_result_txt" file="smol/out-smol-base.tsv" /> |
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255 </test> |
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256 |
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257 <test> |
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258 <!-- |
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259 #8 test for delta in ppm |
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261 <param name="ionization" value="[M+?]+" /> |
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262 <param name="mzdecimal" value="3" /> |
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263 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> |
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264 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> |
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265 <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" /> |
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266 <param name="fragment_match_delta" value="8.542" /> |
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267 <output name="frag_result_txt" file="smol/out-smol-delta-8.542.tsv" /> |
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268 </test> |
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269 |
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270 <test> |
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271 <!-- |
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272 #9 test for delta in m/z |
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274 <param name="ionization" value="[M+?]+" /> |
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275 <param name="mzdecimal" value="3" /> |
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276 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> |
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277 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> |
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278 <param name="peaklist_preco_tsv" value="smol/smol_precursors.tsv" /> |
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279 <param name="fragment_match_delta" value="0.05" /> |
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280 <param name="fragment_match_delta_unit" value="mz" /> |
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281 <output name="frag_result_txt" file="smol/out-smol-delta-0.05mz.tsv" /> |
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282 </test> |
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284 <!-- === expected to fail tests === --> |
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285 <test expect_exit_code="2" expect_failure="true"> |
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286 <!-- |
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287 #10 This test uses old format for molecules file. |
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288 Is is expected to fail |
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289 --> |
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290 <param name="compound_txt" value="compounds_pos_old_format.txt" /> |
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291 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> |
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292 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> |
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293 <assert_stderr> |
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294 <has_line line="Error: Some columns are missing: compound_name, rtsec, inchikey" /> |
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295 </assert_stderr> |
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296 </test> |
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297 |
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298 </tests> |
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299 <help> |
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300 <![CDATA[ |
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301 @AUTHORS@ |
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302 |
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303 ============== |
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304 MS2 validation |
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305 ============== |
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306 |
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307 ----------- |
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308 Description |
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309 ----------- |
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310 |
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311 MS2snoop use results of msPurity to find spectra of standards listed in |
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312 a compounds file. Check the fragments and precursor using correlation of |
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313 among the different scans of fragments |
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314 |
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315 ----------------- |
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316 Workflow position |
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317 ----------------- |
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318 |
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319 -------------- |
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320 Upstream tools |
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321 -------------- |
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322 |
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323 +-------------------------+-----------------+--------+------------+ |
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324 | Name | output file | format | parameter | |
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325 +=========================+=================+========+============+ |
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326 | msPurity.purityA | NA | TSV | NA | |
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327 +-------------------------+-----------------+--------+------------+ |
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328 | msPurity.frag4feature | NA | TSV | NA | |
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329 +-------------------------+-----------------+--------+------------+ |
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330 |
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331 ---------------- |
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332 Downstream tools |
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333 ---------------- |
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334 |
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335 +-------------------------+-----------------+--------+------------+ |
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336 | Name | output file | format | parameter | |
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337 +=========================+=================+========+============+ |
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338 | NA | NA | NA | NA | |
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339 +-------------------------+-----------------+--------+------------+ |
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340 |
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341 |
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342 ----------- |
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343 Input files |
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344 ----------- |
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345 |
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346 +----------------------------------------------+------------+ |
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347 | Parameter : num + label | Format | |
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348 +===========================+==================+============+ |
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349 | Input from msPurity Precursor | TSV,CSV | |
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350 +----------------------------------------------+------------+ |
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351 | Input from msPurity fragment | TSV,CSV | |
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352 | Input compounds file to search in precursor | | |
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353 +----------------------------------------------+------------+ |
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354 | and fragment (Name + m/z + ret Time) | TSV,CSV | |
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355 +----------------------------------------------+------------+ |
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356 |
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357 @PARAMETERS@ |
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358 @OUTPUTS@ |
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359 @CHANGELOG@ |
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360 ]]> |
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361 </help> |
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362 </tool> |