Mercurial > repos > fgiacomoni > hmdb_ms_search

annotate wsdl_hmdb.xml @ 14:625fa968d99a draft

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author fgiacomoni
date Thu, 10 Jan 2019 09:10:14 -0500
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children beb9619263b0
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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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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
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38 ]]></command>
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39 <inputs>
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40 <conditional name="input_type">
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41 <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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42 <option value="YES">YES</option>
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43 <option value="NO">NO</option>
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44 </param>
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45 <when value="YES">
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46 <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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47 <conditional name="header">
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48 <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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49 <option value="no">NO</option>
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50 <option value="yes" selected="true">YES</option>
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51 </param>
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52 <when value="yes">
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53 <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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54 </when>
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55 <when value="no"/>
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56 </conditional>
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57 <param name="colfactor" label="Column of masses " type="data_column" data_ref="masses" accept_default="true" />
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58 </when>
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59 <when value="NO">
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60 <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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61 </when>
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62 </conditional>
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63
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64 <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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65 <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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66 <param name="mode" label="Molecular Species " type="select" display="radio" help="">
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67 <option value="positive">Positif Mode</option>
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68 <option value="negative">Negatif Mode</option>
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69 <option value="neutral" selected="True">Neutral Mass</option>
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70 </param>
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71 </inputs>
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72
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73 <outputs>
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74 <data name="variableMetadata" format="tabular" label="${input_type.masses.name[:-6]}.HMDB.tabular">
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75 <filter>input_type['choice'] == "YES"</filter>
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76 </data>
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77 <data name="HmdbOutWeb" format="html" label="${input_type.masses.name[:-6]}.HMDB_WEB.html">
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78 <filter>input_type['choice'] == "YES"</filter>
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79 </data>
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80 <data name="HmdbOutXlsx" label="${input_type.masses.name[:-6]}.HMDB_XLS.txt" format="tabular">
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81 <filter>input_type['choice'] == "YES"</filter>
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82 </data>
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83 <data name="variableMetadata2" format="tabular" label="HMDB.tabular">
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84 <filter>input_type['choice'] == "NO"</filter>
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85 </data>
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86 <data name="HmdbOutWeb2" format="html" label="HMDB_WEB.html">
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87 <filter>input_type['choice'] == "NO"</filter>
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88 </data>
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89 <data name="HmdbOutXlsx2" label="HMDB_XLS.txt" format="tabular">
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90 <filter>input_type['choice'] == "NO"</filter>
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91 </data>
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92 </outputs>
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93
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94 <tests>
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95 <!--test 01 no result - fake-mzrt-input-with-id -->
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96 <!--
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97 <test>
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98 <param name="choice" value="YES"/>
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99 <param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/>
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100 <param name="header_choice" value="yes"/>
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101 <param name="nblineheader" value="1"/>
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102 <param name="colfactor" value="2"/>
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103 <param name="delta" value="0.001"/>
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104 <param name="mode" value="neutral"/>
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105 <param name="maxquery" value="5"/>
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106 <output name="variableMetadata" file="out_test01.tabular"/>
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107 <output name="HmdbOutWeb" file="out_test01.html"/>
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108 <output name="HmdbOutXlsx" file="out_test01.txt"/>
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109 </test>
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110 -->
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111 <!--test 02 : some results - with-mzrt-input-with-id file-->
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112 <!--
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113 <test>
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114 <param name="choice" value="YES"/>
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115 <param name="masses" value="input_test02_mzrt-input-with-id.tabular"/>
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116 <param name="header_choice" value="yes"/>
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117 <param name="nblineheader" value="1"/>
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118 <param name="colfactor" value="2"/>
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119 <param name="delta" value="0.001"/>
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120 <param name="mode" value="positive"/>
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121 <param name="maxquery" value="5"/>
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122 <output name="variableMetadata" file="out_test02.tabular"/>
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123 <output name="HmdbOutWeb" file="out_test02.html"/>
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124 <output name="HmdbOutXlsx" file="out_test02.txt"/>
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125 </test>
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126 -->
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127 <!--test 03 : some results - with-mz list in manual mass mode-->
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128 <test>
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129 <param name="choice" value="NO"/>
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130 <param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/>
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131 <param name="delta" value="0.05"/>
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132 <param name="mode" value="positive"/>
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133 <param name="maxquery" value="5"/>
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134 <output name="variableMetadata2" file="out_test03.tabular"/>
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135 <output name="HmdbOutWeb2" file="out_test03.html"/>
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136 <output name="HmdbOutXlsx2" file="out_test03.txt"/>
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137 </test>
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138 </tests>
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139
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140 <help><![CDATA[
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141
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142 .. class:: infomark
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143
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144 **Authors** Marion Landi and Franck Giacomoni
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145
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146 ---------------------------------------------------
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147
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148 .. class:: infomark
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149
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150 **Please cite** If you use this tool, please add the following reference
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151 | 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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152 | 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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153
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154
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155 ---------------------------------------------------
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156
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157 ==============
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158 HMDB MS search
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159 ==============
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160
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161 -----------
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162 Description
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163 -----------
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164
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165 | Search informations (like : HMDB id, Name, Adduct, delta mass) on HMDB online bank
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166 | with one or more mass(es) in a file or entered manually
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167
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168
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169 -----------------
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170 Workflow position
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171 -----------------
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172
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173
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174 .. image:: ./static/images/metabolomics/hmdb.png
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175 :width: 800
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176
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177
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178 -----------
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179 Input files
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180 -----------
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181
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182
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183 +-------------------------+-----------+
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184 | Parameter : num + label | Format |
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185 +=========================+===========+
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186 | 1 : File of masses | tabular |
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187 +-------------------------+-----------+
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188
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189 File of masses (Generally variable metadata file) must have at least the following column :
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190 * Masses : column with all the masses in the tsv input file
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191
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192 ----------
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193 Parameters
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194 ----------
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195
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196 Would you use a file
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197 | Choose whether the masses are in a file or entered manually
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198 | YES (default) : parameters **File of masses ; Do you have a header ; Column of masses** are visible
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199 | NO : parameter **Mass to submit** is visible
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200 |
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201
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202
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203 If 'use file'='YES'
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204
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205 File of masses
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206 | see "Input files" section above
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207 | Tabular file format, Generally variable metadata file
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208 |
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209
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210 Do you have a header
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211 | YES (default) : parameter **Number of header lines** is visible
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212 | NO : all lines are considered to contain masses
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213 |
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214
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215 If 'have a header'='YES'
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216
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217 Number of header lines
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218 | Number of lines not containing masses values, these lines will be ignored
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219 |
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220
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221 In all header cases :
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222
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223 Column of masses
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224 | Specify the column number for the mass in the tsv input file
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225 |
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226
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227
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228 If 'use file'='NO'
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229
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230 Mass to submit
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231 | Specify a list of mass to request
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232 | one or more mass(es) entered manually
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233 | For a masses list, writes : m1 m2 m3
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234 | You must separate yours values with space
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235 | dot (.) is for float number
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236 |
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237
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238 In all cases :
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239
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240 Mass-to-charge ratio
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241 | 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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242 |
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243
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244 Molecular Species
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245 | Type of ionization of the molecule : *positif, negatif, neutral*
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246 |
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247
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248
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249 ------------
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250 Output files
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251 ------------
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252
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253 Two types of files
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254 | HMDB_WEB.HTML: for viewing result via HTML.
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255 |
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256 | HMDB_TABULAR.tabular: for linking with others modules.
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257 |
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258 | HMDB_XLS.txt: an excel-like output permitting manual annotation cleaning.
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259 |
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260
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261 ---------------------------------------------------
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262
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263
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264 ---------------
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265 Working example
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266 ---------------
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267
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268
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269 .. class:: warningmark
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270
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271 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
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272 | Format Data For Postprocessing
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273 | Perform LCMS Annotations
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274
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275 .. class:: warningmark
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276
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277 And their "W4M courses 2018":
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278 | Using Galaxy4Metabolomics - W4M table format for Galaxy
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279 | Annotation Banks - Annotation
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280
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281
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282 ]]></help>
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283 <!-- [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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284 <citations>
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285 <citation type="doi">10.1093/nar/gks1065</citation>
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286 <citation type="doi">10.1093/nar/gkx1089</citation>
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287 </citations>
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288 </tool>