Mercurial > repos > fgiacomoni > hmdb_ms_search
annotate wsdl_hmdb.xml @ 20:b5a1d5e43685 draft
Master branch Updating - - Fxx
author | fgiacomoni |
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date | Wed, 23 Jan 2019 07:49:34 -0500 |
parents | ec7c05889e67 |
children | 63ba1cb240b7 |
rev | line source |
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18 | 1 <tool id="wsdl_hmdb" name="HMDB MS search" version="1.6.0"> |
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2 <description> |
14 | 3 search by masses on HMDB online LCMS bank |
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4 </description> |
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5 |
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6 <requirements> |
12 | 7 <requirement type="package" version="2.161">perl-data-dumper</requirement> |
10 | 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> |
9 | 12 <requirement type="package" version="1.74">perl-uri</requirement> |
13 <requirement type="package" version="1.97">perl-text-csv</requirement> | |
14 <requirement type="package" version="3.52">perl-xml-twig</requirement> | |
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15 </requirements> |
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16 |
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17 <stdio> |
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18 <exit_code range="1" level="fatal" /> |
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19 </stdio> |
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20 |
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21 |
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22 <command><![CDATA[ |
13 | 23 perl $__tool_directory__/wsdl_hmdb.pl |
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24 #if str($input_type.choice) == "YES": |
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25 -masses "${input_type.masses}" |
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26 -header_choice "${input_type.header.header_choice}" |
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27 #if str($input_type.header.header_choice) == "yes": |
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28 -nblineheader "${$input_type.header.nbHeader}" |
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29 #end if |
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30 -colfactor "${input_type.colfactor}" |
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31 -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xls "$HmdbOutXlsx" |
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32 #else: |
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33 -mass "${input_type.mass}" |
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34 -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xls "$HmdbOutXlsx2" |
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35 #end if |
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36 -delta "$delta" -mode "$mode" -maxquery "$maxquery" |
15 | 37 -advancedFeatures "$advancedFeatures" |
38 -verbose "$verbose" | |
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39 |
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40 ]]></command> |
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41 <inputs> |
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42 <conditional name="input_type"> |
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43 <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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44 <option value="YES">YES</option> |
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45 <option value="NO">NO</option> |
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46 </param> |
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47 <when value="YES"> |
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48 <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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49 <conditional name="header"> |
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50 <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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51 <option value="no">NO</option> |
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52 <option value="yes" selected="true">YES</option> |
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53 </param> |
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54 <when value="yes"> |
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55 <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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56 </when> |
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57 <when value="no"/> |
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58 </conditional> |
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59 <param name="colfactor" label="Column of masses " type="data_column" data_ref="masses" accept_default="true" /> |
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60 </when> |
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61 <when value="NO"> |
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62 <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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63 </when> |
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64 </conditional> |
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65 |
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66 <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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67 <param name="maxquery" label="Number of maximum entries returned by the query " type="integer" value="20" min="1" max="50" size="10" help="Default value is 20 for each queried mz / max is 50"/> |
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68 <param name="mode" label="Molecular Species " type="select" display="radio" help=""> |
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69 <option value="positive">Positif Mode</option> |
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70 <option value="negative">Negatif Mode</option> |
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71 <option value="neutral" selected="True">Neutral Mass</option> |
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72 </param> |
15 | 73 <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"> |
74 <option value="1">Advanced mode</option> | |
75 <option value="0" selected="True">Default mode</option> | |
76 </param> | |
77 <param name="verbose" type="select" label="Verbose level" display="radio" help=""> | |
78 <option value="1" selected="true">Low</option> | |
79 <option value="3" >High</option> | |
80 </param> | |
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81 </inputs> |
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82 |
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83 <outputs> |
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84 <data name="variableMetadata" format="tabular" label="${input_type.masses.name[:-6]}.HMDB.tabular"> |
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85 <filter>input_type['choice'] == "YES"</filter> |
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86 </data> |
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87 <data name="HmdbOutWeb" format="html" label="${input_type.masses.name[:-6]}.HMDB_WEB.html"> |
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88 <filter>input_type['choice'] == "YES"</filter> |
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89 </data> |
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90 <data name="HmdbOutXlsx" label="${input_type.masses.name[:-6]}.HMDB_XLS.txt" format="tabular"> |
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91 <filter>input_type['choice'] == "YES"</filter> |
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92 </data> |
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93 <data name="variableMetadata2" format="tabular" label="HMDB.tabular"> |
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94 <filter>input_type['choice'] == "NO"</filter> |
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95 </data> |
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96 <data name="HmdbOutWeb2" format="html" label="HMDB_WEB.html"> |
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97 <filter>input_type['choice'] == "NO"</filter> |
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98 </data> |
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99 <data name="HmdbOutXlsx2" label="HMDB_XLS.txt" format="tabular"> |
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100 <filter>input_type['choice'] == "NO"</filter> |
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101 </data> |
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102 </outputs> |
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103 |
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104 <tests> |
14 | 105 <!--test 01 no result - fake-mzrt-input-with-id --> |
106 <!-- | |
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107 <test> |
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108 <param name="choice" value="YES"/> |
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109 <param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/> |
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110 <param name="header_choice" value="yes"/> |
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111 <param name="nblineheader" value="1"/> |
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112 <param name="colfactor" value="2"/> |
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113 <param name="delta" value="0.001"/> |
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114 <param name="mode" value="neutral"/> |
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115 <param name="maxquery" value="5"/> |
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116 <output name="variableMetadata" file="out_test01.tabular"/> |
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117 <output name="HmdbOutWeb" file="out_test01.html"/> |
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118 <output name="HmdbOutXlsx" file="out_test01.txt"/> |
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119 </test> |
14 | 120 --> |
121 <!--test 02 : some results - with-mzrt-input-with-id file--> | |
122 <!-- | |
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123 <test> |
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124 <param name="choice" value="YES"/> |
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125 <param name="masses" value="input_test02_mzrt-input-with-id.tabular"/> |
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126 <param name="header_choice" value="yes"/> |
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127 <param name="nblineheader" value="1"/> |
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128 <param name="colfactor" value="2"/> |
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129 <param name="delta" value="0.001"/> |
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130 <param name="mode" value="positive"/> |
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131 <param name="maxquery" value="5"/> |
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132 <output name="variableMetadata" file="out_test02.tabular"/> |
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133 <output name="HmdbOutWeb" file="out_test02.html"/> |
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134 <output name="HmdbOutXlsx" file="out_test02.txt"/> |
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135 </test> |
14 | 136 --> |
137 <!--test 03 : some results - with-mz list in manual mass mode--> | |
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138 <test> |
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139 <param name="choice" value="NO"/> |
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140 <param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/> |
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141 <param name="delta" value="0.05"/> |
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142 <param name="mode" value="positive"/> |
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143 <param name="maxquery" value="5"/> |
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144 <output name="variableMetadata2" file="out_test03.tabular"/> |
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145 <output name="HmdbOutWeb2" file="out_test03.html"/> |
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146 <output name="HmdbOutXlsx2" file="out_test03.txt"/> |
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147 </test> |
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148 </tests> |
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149 |
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150 <help><![CDATA[ |
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151 |
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152 .. class:: infomark |
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153 |
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154 **Authors** Marion Landi and Franck Giacomoni |
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155 |
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156 --------------------------------------------------- |
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157 |
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158 .. class:: infomark |
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159 |
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160 **Please cite** If you use this tool, please add the following reference |
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161 | 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. |
14 | 162 | 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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163 |
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164 |
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165 --------------------------------------------------- |
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166 |
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167 ============== |
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168 HMDB MS search |
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169 ============== |
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170 |
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171 ----------- |
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172 Description |
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173 ----------- |
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174 |
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175 | Search informations (like : HMDB id, Name, Adduct, delta mass) on HMDB online bank |
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176 | with one or more mass(es) in a file or entered manually |
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177 |
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178 |
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179 ----------------- |
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180 Workflow position |
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181 ----------------- |
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182 |
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183 |
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184 .. image:: ./static/images/metabolomics/hmdb.png |
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185 :width: 800 |
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186 |
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187 |
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188 ----------- |
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189 Input files |
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190 ----------- |
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191 |
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192 |
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193 +-------------------------+-----------+ |
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194 | Parameter : num + label | Format | |
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195 +=========================+===========+ |
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196 | 1 : File of masses | tabular | |
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197 +-------------------------+-----------+ |
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198 |
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199 File of masses (Generally variable metadata file) must have at least the following column : |
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200 * Masses : column with all the masses in the tsv input file |
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201 |
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202 ---------- |
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203 Parameters |
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204 ---------- |
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205 |
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206 Would you use a file |
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207 | Choose whether the masses are in a file or entered manually |
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208 | YES (default) : parameters **File of masses ; Do you have a header ; Column of masses** are visible |
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209 | NO : parameter **Mass to submit** is visible |
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210 | |
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211 |
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212 |
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213 If 'use file'='YES' |
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214 |
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215 File of masses |
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216 | see "Input files" section above |
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217 | Tabular file format, Generally variable metadata file |
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218 | |
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219 |
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220 Do you have a header |
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221 | YES (default) : parameter **Number of header lines** is visible |
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222 | NO : all lines are considered to contain masses |
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223 | |
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224 |
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225 If 'have a header'='YES' |
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226 |
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227 Number of header lines |
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228 | Number of lines not containing masses values, these lines will be ignored |
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229 | |
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230 |
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231 In all header cases : |
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232 |
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233 Column of masses |
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234 | Specify the column number for the mass in the tsv input file |
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235 | |
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236 |
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237 |
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238 If 'use file'='NO' |
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239 |
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240 Mass to submit |
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241 | Specify a list of mass to request |
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242 | one or more mass(es) entered manually |
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243 | For a masses list, writes : m1 m2 m3 |
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244 | You must separate yours values with space |
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245 | dot (.) is for float number |
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246 | |
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247 |
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248 In all cases : |
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249 |
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250 Mass-to-charge ratio |
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251 | 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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252 | |
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253 |
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254 Molecular Species |
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255 | Type of ionization of the molecule : *positif, negatif, neutral* |
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256 | |
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257 |
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258 |
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259 ------------ |
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260 Output files |
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261 ------------ |
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262 |
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263 Two types of files |
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264 | HMDB_WEB.HTML: for viewing result via HTML. |
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265 | |
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266 | HMDB_TABULAR.tabular: for linking with others modules. |
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267 | |
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268 | HMDB_XLS.txt: an excel-like output permitting manual annotation cleaning. |
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269 | |
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270 |
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271 --------------------------------------------------- |
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272 |
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273 |
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274 --------------- |
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275 Working example |
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276 --------------- |
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277 |
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278 |
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279 .. class:: warningmark |
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280 |
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281 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto |
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282 | Format Data For Postprocessing |
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283 | Perform LCMS Annotations |
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284 |
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285 .. class:: warningmark |
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286 |
14 | 287 And their "W4M courses 2018": |
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288 | Using Galaxy4Metabolomics - W4M table format for Galaxy |
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289 | Annotation Banks - Annotation |
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290 |
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291 |
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292 ]]></help> |
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293 <!-- [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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294 <citations> |
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295 <citation type="doi">10.1093/nar/gks1065</citation> |
14 | 296 <citation type="doi">10.1093/nar/gkx1089</citation> |
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297 </citations> |
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298 </tool> |