Mercurial > repos > fgiacomoni > hmdb_ms_search

annotate wsdl_hmdb.xml @ 17:49f87ddb2c78 draft

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author fgiacomoni
date Wed, 23 Jan 2019 02:57:07 -0500
parents beb9619263b0
children ec7c05889e67
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1 <tool id="wsdl_hmdb" name="HMDB MS search" version="2018-10-01">
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2 <description>
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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>
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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="1.74">perl-uri</requirement>
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13 <requirement type="package" version="1.97">perl-text-csv</requirement>
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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[
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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"
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37 -advancedFeatures "$advancedFeatures"
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38 -verbose "$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>
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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">
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74 <option value="1">Advanced mode</option>
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75 <option value="0" selected="True">Default mode</option>
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76 </param>
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77 <param name="verbose" type="select" label="Verbose level" display="radio" help="">
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78 <option value="1" selected="true">Low</option>
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79 <option value="3" >High</option>
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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>
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105 <!--test 01 no result - fake-mzrt-input-with-id -->
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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>
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120 -->
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121 <!--test 02 : some results - with-mzrt-input-with-id file-->
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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>
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136 -->
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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.
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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
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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>
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296 <citation type="doi">10.1093/nar/gkx1089</citation>
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297 </citations>
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298 </tool>