annotate wsdl_hmdb.xml @ 28:6d796927335d draft

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1 <tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.5">
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2 <description>
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3 search by masses on HMDB v5 online LCMS bank
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4 </description>
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5
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6 <requirements>
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7 <requirement type="package" version="2.161">perl-data-dumper</requirement>
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8 <requirement type="package" version="2.97">perl-html-template</requirement>
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9 <requirement type="package" version="1.19">perl-soap-lite</requirement>
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10 <requirement type="package" version="6.15">perl-lwp-simple</requirement>
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11 <requirement type="package" version="6.15">perl-libwww-perl</requirement>
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12 <requirement type="package" version="5.17">perl-uri</requirement>
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13 <requirement type="package" version="1.1.1">perl-uri-encode</requirement>
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14 <requirement type="package" version="1.97">perl-text-csv</requirement>
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15 <requirement type="package" version="3.52">perl-xml-twig</requirement>
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16 <requirement type="package" version="1.91">perl-www-mechanize</requirement>
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17 </requirements>
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18
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19 <stdio>
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20 <exit_code range="1" level="fatal" />
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21 </stdio>
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22
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23
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24 <command><![CDATA[
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25 perl $__tool_directory__/wsdl_hmdb.pl
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26 #if str($input_type.choice) == "YES":
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27 -masses "${input_type.masses}"
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28 -header_choice "${input_type.header.header_choice}"
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29 #if str($input_type.header.header_choice) == "yes":
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30 -nblineheader "${$input_type.header.nbHeader}"
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31 #end if
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32 -colfactor "${input_type.colfactor}"
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33 -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xlsx "$HmdbOutXlsx"
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34 #else:
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35 -mass "${input_type.mass}"
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36 -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xlsx "$HmdbOutXlsx2"
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37 #end if
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38
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39 -mode "${mode_type.mode}"
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40
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41 #if str($mode_type.mode) == "positive":
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42 -adduct_type "${mode_type.data_positive_adducts}"
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43 #elif str($mode_type.mode) == "negative":
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44 -adduct_type "${mode_type.data_negative_adducts}"
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45 #elif str($mode_type.mode) == "neutral":
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46 -adduct_type "${mode_type.data_neutral_adducts}"
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47 #end if
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48
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49 -delta "$delta" -maxquery "$maxquery"
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50 -advancedFeatures "$advancedFeatures"
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51 -verbose "$verbose"
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52
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53 ]]></command>
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54 <inputs>
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55 <conditional name="input_type">
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56 <param name="choice" type="select" label="Would you use a file " help="if 'NO' is selected then one or more mass(es) must be entered manually">
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57 <option value="YES">YES</option>
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58 <option value="NO">NO</option>
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59 </param>
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60 <when value="YES">
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61 <param name="masses" label="File of masses (Variable Metadata) " format="tabular" type="data" help="Generally variable metadata file. Please note : HMDB allows maximum 700 query masses per request" />
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62 <conditional name="header">
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63 <param name="header_choice" type="select" label="Do you have a header " help="if 'YES' is selected then enter your number of header lines">
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64 <option value="no">NO</option>
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65 <option value="yes" selected="true">YES</option>
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66 </param>
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67 <when value="yes">
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68 <param name="nbHeader" label="Number of header lines " type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/>
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69 </when>
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70 <when value="no"/>
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71 </conditional>
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72 <param name="colfactor" label="Column of masses " type="data_column" data_ref="masses" accept_default="true" />
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73 </when>
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74 <when value="NO">
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75 <param name="mass" label="Mass to submit " type="text" size="20" help="For a masses list, writes : m1 m2 m3. Your values must be separated by spaces. You should use dot (.) like decimal separator" />
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76 </when>
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77 </conditional>
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78
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79 <param name="delta" label="Mass-to-charge ratio " type="float" value="0.05" min="0" max="10" size="10" help="Default value is 0.05 for HMDB (mass-to-charge ratio)"/>
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80 <param name="maxquery" label="Number of maximum entries returned by the query " type="integer" value="10" min="1" max="50" size="10" help="Default value is 10 for each queried mz / max is 50"/>
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81
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82 <conditional name="mode_type">
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83 <param name="mode" label="Molecular Species " type="select" display="radio" help="">
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84 <option value="positive">Positif Mode</option>
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85 <option value="negative">Negatif Mode</option>
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86 <option value="neutral" selected="True">Neutral Mass</option>
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87 </param>
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88 <when value="positive">
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89 <param name="data_positive_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
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90 <option value="Unknown">Unknown</option>
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91 <option value="M+H" selected="True">M+H</option>
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92 <option value="M+H-2H2O">M+H-2H2O</option>
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93 <option value="M+H-H2O">M+H-H2O</option>
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94 <option value="M+NH4-H2O">M+NH4-H2O</option>
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95 <option value="M+Li">M+Li</option>
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96 <option value="M+NH4">M+NH4</option>
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97 <option value="M+Na">M+Na</option>
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98 <option value="M+CH3OH+H">M+CH3OH+H</option>
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99 <option value="M+K">M+K</option>
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100 <option value="M+ACN+H">M+ACN+H</option>
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101 <option value="M+2Na-H">M+2Na-H</option>
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102 <option value="M+IsoProp+H">M+IsoProp+H</option>
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103 <option value="M+ACN+Na">M+ACN+Na</option>
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104 <option value="M+2K-H">M+2K-H</option>
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105 <option value="M+DMSO+H">M+DMSO+H</option>
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106 <option value="M+2ACN+H">M+2ACN+H</option>
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107 <option value="M+IsoProp+Na+H">M+IsoProp+Na+H</option>
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108 <option value="M+H+HCOONa">M+H+HCOONa</option>
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109 <option value="2M+H">2M+H</option>
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110 <option value="2M+NH4">2M+NH4</option>
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111 <option value="2M+Na">2M+Na</option>
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112 <option value="2M+2H+3H2O">2M+2H+3H2O</option>
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113 <option value="2M+K">2M+K</option>
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114 <option value="2M+ACN+H">2M+ACN+H</option>
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115 <option value="2M+ACN+Na">2M+ACN+Na</option>
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116 <option value="2M+H-H2O">2M+H-H2O</option>
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117 <option value="M+2H">M+2H</option>
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118 <option value="M+H+NH4">M+H+NH4</option>
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119 <option value="M+H+Na">M+H+Na</option>
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120 <option value="M+H+K">M+H+K</option>
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121 <option value="M+ACN+2H">M+ACN+2H</option>
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122 <option value="M+2Na">M+2Na</option>
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123 <option value="M+2ACN+2H">M+2ACN+2H</option>
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124 <option value="M+3ACN+2H">M+3ACN+2H</option>
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125 <option value="M+3H">M+3H</option>
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126 <option value="M+2H+Na">M+2H+Na</option>
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127 <option value="M+H+2Na">M+H+2Na</option>
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128 <option value="M+3Na">M+3Na</option>
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129 <option value="M+H+2K">M+H+2K</option>
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130 </param>
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131 </when>
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132 <when value="negative">
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133 <param name="data_negative_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
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134 <option value="Unknown">Unknown</option>
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135 <option value="M-H" selected="True">M-H</option>
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136 <option value="M-H20-H">M-H20-H</option>
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137 <option value="M+F">M+F</option>
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138 <option value="M+Na-2H">M+Na-2H</option>
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139 <option value="M+Cl">M+Cl</option>
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140 <option value="M+K-2H">M+K-2H</option>
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141 <option value="M+FA-H">M+FA-H</option>
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142 <option value="M+Hac-H">M+Hac-H</option>
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143 <option value="M+Br">M+Br</option>
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144 <option value="M+TFA-H">M+TFA-H</option>
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145 <option value="M-H+HCOONa">M-H+HCOONa</option>
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146 <option value="2M-H">2M-H</option>
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147 <option value="2M+FA-H">2M+FA-H</option>
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148 <option value="2M+Hac-H">2M+Hac-H</option>
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149 <option value="3M-H">3M-H</option>
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150 <option value="M-2H">M-2H</option>
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151 <option value="M-3H">M-3H</option>
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152 </param>
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153 </when>
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154 <when value="neutral">
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155 <param name="data_neutral_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
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156 <option value="Unknown">Unknown</option>
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157 <option value="M" selected="True">M</option>
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158 </param>
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159 </when>
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160 </conditional>
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161
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162
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163
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164
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165 <param name="advancedFeatures" label="Performing advanced annotation " type="select" display="radio" help="Getting more information from HMDB (Inchi, logP, ...) but increase time of tool execution">
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166 <option value="1">Advanced mode</option>
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167 <option value="0" selected="True">Default mode</option>
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168 </param>
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169 <param name="verbose" type="select" label="Verbose level" display="radio" help="">
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170 <option value="1" selected="true">Low</option>
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171 <option value="3" >High</option>
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172 </param>
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173 </inputs>
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174
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175 <outputs>
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176 <data name="variableMetadata" format="tabular" label="${input_type.masses.name[:-6]}.HMDB.tabular">
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177 <filter>input_type['choice'] == "YES"</filter>
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178 </data>
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179 <data name="HmdbOutWeb" format="html" label="${input_type.masses.name[:-6]}.HMDB_WEB.html">
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180 <filter>input_type['choice'] == "YES"</filter>
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181 </data>
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182 <data name="HmdbOutXlsx" label="${input_type.masses.name[:-6]}.HMDB_XLS.txt" format="tabular">
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183 <filter>input_type['choice'] == "YES"</filter>
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184 </data>
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185 <data name="variableMetadata2" format="tabular" label="HMDB.tabular">
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186 <filter>input_type['choice'] == "NO"</filter>
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187 </data>
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188 <data name="HmdbOutWeb2" format="html" label="HMDB_WEB.html">
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189 <filter>input_type['choice'] == "NO"</filter>
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190 </data>
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191 <data name="HmdbOutXlsx2" label="HMDB_XLS.txt" format="tabular">
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192 <filter>input_type['choice'] == "NO"</filter>
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193 </data>
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194 </outputs>
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195
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196 <tests>
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197 <!--test 01 no result - fake-mzrt-input-with-id -->
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198 <!--
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199 <test>
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200 <param name="choice" value="YES"/>
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201 <param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/>
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202 <param name="header_choice" value="yes"/>
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203 <param name="nblineheader" value="1"/>
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204 <param name="colfactor" value="2"/>
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205 <param name="delta" value="0.001"/>
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206 <param name="mode" value="neutral"/>
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207 <param name="maxquery" value="5"/>
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208 <output name="variableMetadata" file="out_test01.tabular"/>
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209 <output name="HmdbOutWeb" file="out_test01.html"/>
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210 <output name="HmdbOutXlsx" file="out_test01.txt"/>
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211 </test>
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212 -->
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213 <!--test 02 : some results - with-mzrt-input-with-id file-->
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214 <!--
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215 <test>
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216 <param name="choice" value="YES"/>
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217 <param name="masses" value="input_test02_mzrt-input-with-id.tabular"/>
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218 <param name="header_choice" value="yes"/>
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219 <param name="nblineheader" value="1"/>
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220 <param name="colfactor" value="2"/>
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221 <param name="delta" value="0.001"/>
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222 <param name="mode" value="positive"/>
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223 <param name="maxquery" value="5"/>
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224 <output name="variableMetadata" file="out_test02.tabular"/>
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225 <output name="HmdbOutWeb" file="out_test02.html"/>
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226 <output name="HmdbOutXlsx" file="out_test02.txt"/>
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227 </test>
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228 -->
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229 <!--test 03 : some results - with-mz list in manual mass mode-->
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230 <test>
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231 <param name="choice" value="NO"/>
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232 <param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/>
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233 <param name="delta" value="0.05"/>
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234 <param name="mode" value="positive"/>
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235 <param name="maxquery" value="5"/>
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236 <param name="data_positive_adducts" value="M+H"/>
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237 <output name="variableMetadata2" file="out_test03.tabular"/>
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238 <output name="HmdbOutWeb2" file="out_test03.html"/>
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239 <output name="HmdbOutXlsx2" file="out_test03.txt"/>
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240 </test>
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241 </tests>
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242
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243 <help><![CDATA[
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244
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245 .. class:: infomark
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246
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247 **Authors** Marion Landi, Yann Guitton and Franck Giacomoni
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248
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249 ---------------------------------------------------
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250
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251 .. class:: infomark
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252
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253 **Please cite** If you use this tool, please add the following reference
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254 | Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res. 2013.
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255 | Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, et al., HMDB 4.0 — The Human Metabolome Database for 2018. Nucleic Acids Res. 2018.
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256 | Wishart DS et al, HMDB 5.0 - the Human Metabolome Database for 2022, Nucleic Acids Res. 2022.
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257
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258
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259 ---------------------------------------------------
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260
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261 ==============
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262 HMDB MS search
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263 ==============
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264
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265 -----------
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266 Description
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267 -----------
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268
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269 | Search informations (like : HMDB id, Name, Adduct, delta mass) on HMDB online bank
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270 | with one or more mass(es) in a file or entered manually
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271
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272
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273 -----------------
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274 Workflow position
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275 -----------------
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276
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277
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278 .. image:: ./static/images/metabolomics/hmdb.png
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279 :width: 800
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280
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281
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282 -----------
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283 Input files
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284 -----------
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285
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286
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287 +-------------------------+-----------+
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288 | Parameter : num + label | Format |
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289 +=========================+===========+
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290 | 1 : File of masses | tabular |
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291 +-------------------------+-----------+
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292
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293 File of masses (Generally variable metadata file) must have at least the following column :
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294 * Masses : column with all the masses in the tsv input file
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295
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296 ----------
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297 Parameters
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298 ----------
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299
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300 Would you use a file
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301 | Choose whether the masses are in a file or entered manually
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302 | YES (default) : parameters **File of masses ; Do you have a header ; Column of masses** are visible
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303 | NO : parameter **Mass to submit** is visible
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304 |
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305
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306
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307 If 'use file'='YES'
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308
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309 File of masses
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310 | see "Input files" section above
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311 | Tabular file format, Generally variable metadata file
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312 |
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313
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314 Do you have a header
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315 | YES (default) : parameter **Number of header lines** is visible
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316 | NO : all lines are considered to contain masses
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317 |
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318
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319 If 'have a header'='YES'
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320
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321 Number of header lines
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322 | Number of lines not containing masses values, these lines will be ignored
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323 |
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324
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325 In all header cases :
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326
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327 Column of masses
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328 | Specify the column number for the mass in the tsv input file
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329 |
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330
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331
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332 If 'use file'='NO'
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333
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334 Mass to submit
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335 | Specify a list of mass to request
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336 | one or more mass(es) entered manually
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337 | For a masses list, writes : m1 m2 m3
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338 | You must separate yours values with space
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339 | dot (.) is for float number
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340 |
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341
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342 In all cases :
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343
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344 Mass-to-charge ratio
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345 | Specify a delta (mass-to-charge ratio) to apply on mass - This value is a float, between 0.0000000000000001 and 10.
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346 |
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347
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348 Molecular Species
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349 | Type of ionization of the molecule : *positif, negatif, neutral*
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350 |
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351
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352
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353 ------------
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354 Output files
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355 ------------
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356
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357 Two types of files
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358 | HMDB_WEB.HTML: for viewing result via HTML.
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359 |
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360 | HMDB_TABULAR.tabular: for linking with others modules.
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361 |
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362 | HMDB_XLS.txt: an excel-like output permitting manual annotation cleaning.
1
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363 |
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364
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365 ---------------------------------------------------
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366
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367
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368 ---------------
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369 Working example
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370 ---------------
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371
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372
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373 .. class:: warningmark
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374
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375 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
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376 | Format Data For Postprocessing
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377 | Perform LCMS Annotations
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378
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379 .. class:: warningmark
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380
24
d8e2ede293a6 Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx
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381 And their "W4M courses 2022":
1
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382 | Using Galaxy4Metabolomics - W4M table format for Galaxy
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383 | Annotation Banks - Annotation
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384
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385
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386 ]]></help>
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387 <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel -->
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388 <citations>
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389 <citation type="doi">10.1093/nar/gks1065</citation>
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390 <citation type="doi">10.1093/nar/gkx1089</citation>
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391 <citation type="doi">10.1093/nar/gkab1062</citation>
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392 </citations>
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393 </tool>