Mercurial > repos > workflow4metabolomics > ms2snoop

annotate MS2snoop.xml @ 4:856001213966 draft

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planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
author workflow4metabolomics
date Wed, 06 Jul 2022 10:38:39 +0000
parents c68c94865667
children 78d5a12406c2
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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>
1
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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 </requirements>
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20 <stdio>
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21 <exit_code range="1" level="fatal" description="Missing parameter error" />
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22 <exit_code range="2" level="fatal" description="Bad parameter's value" />
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23 <exit_code range="3" level="fatal" description="Missing input file" />
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24 <exit_code range="4:254" level="fatal" description="Unknown error" />
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25 <exit_code range="255" level="fatal" description="No any result to output" />
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26 <regex match="Error in\s+.*:\s+.*" />
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27 </stdio>
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28 <version_command>
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29 Rscript '$__tool_directory__/MS2snoop.R' --version | head -n 1
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30 </version_command>
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31 <command>
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32 <![CDATA[
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33 Rscript '$__tool_directory__/MS2snoop.R'
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34 --output '$frag_result_txt'
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35 --compounds '$compound_txt'
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36 --fragments '$peaklist_frag_tsv'
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37 --precursors '$peaklist_preco_tsv'
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38 --tolmz '$tolmz'
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39 --tolrt '$tolrt'
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40 --seuil_ra '$seuil_ra'
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41 --mzdecimal '$mzdecimal'
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42 --r_threshold '$r_threshold'
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43 --min_number_scan '$min_number_scan'
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44 $advenced.debug
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45 $advenced.verbose
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46 ]]>
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47 </command>
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48 <inputs>
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49 <param
2
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50 argument="--compound_txt"
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51 type="data"
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52 format="tabular,csv,tsv"
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53 label="list of compounds"
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54 help="The table must fit the format: col1=Name of molecule, col2=m/z, col3=retention time"
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55 />
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56 <param
2
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57 argument="--peaklist_frag_tsv"
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58 type="data"
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59 format="tabular,csv,tsv"
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60 label="MSpurity fragments file"
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61 />
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62 <param
2
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63 argument="--peaklist_preco_tsv"
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64 type="data"
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65 format="tabular,csv,tsv"
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66 label="MSpurity precursors file"
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67 />
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68 <param
2
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69 argument="--tolmz"
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70 type="float"
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71 min="0.0001"
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72 max="10"
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73 value="0.01"
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74 label="MZ Tolerence"
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75 />
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76 <param
2
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77 argument="--tolrt"
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78 type="integer"
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79 min="0"
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80 max="30"
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81 value="20"
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82 label="RT Tolerence"
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83 />
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84 <param
2
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85 argument="--seuil_ra"
0
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86 type="float"
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87 min="0"
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88 max="1"
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89 value="0.05"
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90 label="r pearson correlation threshold between precursor and fragment absolute intensity"
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91 />
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92 <param
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93 argument="--mzdecimal"
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94 type="integer"
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95 min="0"
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96 max="5"
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97 value="0"
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98 label="nb decimal for mz"
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99 />
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100 <param
2
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101 argument="--r_threshold"
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102 type="float"
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103 min="0"
1
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104 value="0.85"
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105 label="fragment absolute intensity"
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106 />
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107 <param
2
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108 argument="--min_number_scan"
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109 type="integer"
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110 min="0"
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111 max="25"
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112 value="8"
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113 label="Present in at least X scan"
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114 help="fragments are kept if they are found in a minimum number of scans"
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115 />
1
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116 <section title="Advenced Options" name="advenced">
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117 <param
2
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118 argument="--verbose"
1
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119 type="boolean"
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120 value=""
2
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121 optional="true"
1
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122 label="Verbose logs"
2
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123 help="The tool will print more logs"
1
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124 truevalue="--verbose"
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125 falsevalue=""
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126 />
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127 <param
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128 argument="--debug"
1
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129 type="boolean"
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130 value=""
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131 optional="true"
1
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132 label="Debug statements"
2
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133 help="The tool will print debug statements"
1
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134 truevalue="--debug"
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135 falsevalue=""
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136 />
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137 </section>
0
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138 </inputs>
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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139 <outputs>
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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140 <data
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141 name="frag_result_txt"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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142 format="tabular"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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143 label="compound_fragments_result.txt"
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144 />
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145 </outputs>
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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146 <tests>
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147 <test>
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148 <param name="compound_txt" value="compounds_pos.txt" />
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149 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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150 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
0
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151 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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152 <assert_stdout>
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153 <expand macro="has_regular_stdout"/>
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154 <expand macro="has_not_verbose_stdout"/>
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155 <expand macro="has_not_debug_stdout"/>
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156 </assert_stdout>
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157 </test>
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158 <test>
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159 <param name="compound_txt" value="compounds_pos.txt" />
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160 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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161 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
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162 <param name="verbose" value="--verbose" />
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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_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 <test>
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171 <param name="compound_txt" value="compounds_pos.txt" />
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172 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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173 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
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174 <param name="debug" value="--debug" />
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175 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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176 <assert_stdout>
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177 <expand macro="has_smol_stdout"/>
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178 <expand macro="has_debug_stdout"/>
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179 <expand macro="has_not_verbose_stdout"/>
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180 </assert_stdout>
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181 </test>
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182 <test>
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183 <param name="compound_txt" value="compounds_pos.txt" />
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184 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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185 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
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186 <param name="debug" value="--debug" />
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187 <param name="verbose" value="--verbose" />
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188 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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189 <assert_stdout>
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190 <expand macro="has_smol_stdout"/>
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191 <expand macro="has_debug_stdout"/>
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192 <expand macro="has_smol_verbose_stdout"/>
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193 </assert_stdout>
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194 </test>
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195 <test>
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196 <param name="compound_txt" value="compounds_pos.csv" />
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197 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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198 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
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199 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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200 <assert_stdout>
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201 <expand macro="has_regular_stdout"/>
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202 <expand macro="has_not_verbose_stdout"/>
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203 <expand macro="has_not_debug_stdout"/>
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204 </assert_stdout>
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205 </test>
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206 <test>
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207 <param name="compound_txt" value="compounds_pos.csv" />
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208 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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209 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
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210 <param name="verbose" value="--verbose" />
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211 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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212 <assert_stdout>
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213 <expand macro="has_regular_stdout"/>
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214 <expand macro="has_verbose_stdout"/>
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215 <expand macro="has_not_debug_stdout"/>
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216 </assert_stdout>
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217 </test>
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218 <test>
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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="debug" value="--debug" />
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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_smol_stdout"/>
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226 <expand macro="has_debug_stdout"/>
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227 <expand macro="has_not_verbose_stdout"/>
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228 </assert_stdout>
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229 </test>
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230 <test>
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231 <param name="compound_txt" value="compounds_pos.csv" />
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232 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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233 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
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234 <param name="debug" value="--debug" />
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235 <param name="verbose" value="--verbose" />
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236 <output name="frag_result_txt" file="compound_fragments_result.txt" />
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237 <assert_stdout>
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238 <expand macro="has_smol_stdout"/>
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239 <expand macro="has_debug_stdout"/>
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240 <expand macro="has_smol_verbose_stdout"/>
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241 </assert_stdout>
0
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242 </test>
4
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243 <test expect_exit_code="2" expect_failure="true">
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244 <param name="compound_txt" value="compounds_pos_old_format.txt" />
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245 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
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246 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
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247 <assert_stderr>
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248 <has_line line="Error: Some columns are missing: compound_name, rtsec, inchikey" />
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249 </assert_stderr>
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250 </test>
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251 </tests>
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252 <help><![CDATA[
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253
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254 @AUTHORS@
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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
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265 a compounds file. Check the fragments and precursor using correlation of
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266 among the different scans of fragments
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267
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268 -----------------
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269 Workflow position
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270 -----------------
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271
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272 --------------
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273 Upstream tools
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274 --------------
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275
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276 +-------------------------+-----------------+--------+------------+
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277 | Name | output file | format | parameter |
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278 +=========================+=================+========+============+
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279 | msPurity.purityA | NA | TSV | NA |
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280 +-------------------------+-----------------+--------+------------+
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281 | msPurity.frag4feature | NA | TSV | NA |
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282 +-------------------------+-----------------+--------+------------+
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283
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284 ----------------
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285 Downstream tools
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286 ----------------
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287
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288 +-------------------------+-----------------+--------+------------+
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289 | Name | output file | format | parameter |
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290 +=========================+=================+========+============+
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291 | NA | NA | NA | NA |
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292 +-------------------------+-----------------+--------+------------+
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293
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294
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295 -----------
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296 Input files
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297 -----------
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298
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299 +----------------------------------------------+------------+
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300 | Parameter : num + label | Format |
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301 +===========================+==================+============+
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302 | Input from msPurity Precursor | TSV,CSV |
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303 +----------------------------------------------+------------+
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304 | Input from msPurity fragment | TSV,CSV |
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305 | Input compounds file to search in precursor | |
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306 +----------------------------------------------+------------+
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307 | and fragment (Name + m/z + ret Time) | TSV,CSV |
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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 @OUTPUTS@
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315
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316
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317 @CHANGELOG@
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318
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319 ]]></help>
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320 </tool>