Mercurial > repos > fgiacomoni > hmdb_ms_search

annotate wsdl_hmdb.xml @ 1:6d0a0f8f672a draft

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author fgiacomoni
date Wed, 23 Nov 2016 09:31:50 -0500
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1 <tool id="wsdl_hmdb" name="HMDB MS search" version="2016-11-28">
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2 <description>
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3 search by masses on HMDB online bank
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4 </description>
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5
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6 <requirements>
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7 <!-- Waiting for conda improvement in Galaxy
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8 <requirement type="package" version="1.19">perl-soap-lite</requirement>
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9 <requirement type="package" version="6.15">perl-lwp-simple</requirement>
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10 <requirement type="package" version="6.15">perl-libwww-perl</requirement>
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11 <requirement type="package" version="2.95">perl-html-template</requirement>
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12 <requirement type="package" version="1.71">perl-uri</requirement>
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13 <requirement type="package" version="1.33">perl-text-csv</requirement>
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14 <requirement type="package" version="3.49">perl-xml-twig</requirement>
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15 -->
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16 </requirements>
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17
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18 <stdio>
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19 <exit_code range="1" level="fatal" />
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20 </stdio>
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21
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22
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23 <command><![CDATA[
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24 perl $__tool_directory__/wsdl_hmdb.pl
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25 #if str($input_type.choice) == "YES":
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26 -masses "${input_type.masses}"
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27 -header_choice "${input_type.header.header_choice}"
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28 #if str($input_type.header.header_choice) == "yes":
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29 -nblineheader "${$input_type.header.nbHeader}"
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30 #end if
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31 -colfactor "${input_type.colfactor}"
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32 -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xls "$HmdbOutXlsx"
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33 #else:
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34 -mass "${input_type.mass}"
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35 -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xls "$HmdbOutXlsx2"
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36 #end if
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37 -delta "$delta" -mode "$mode" -maxquery "$maxquery"
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38
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39 ]]></command>
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40 <inputs>
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41 <conditional name="input_type">
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42 <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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43 <option value="YES">YES</option>
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44 <option value="NO">NO</option>
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45 </param>
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46 <when value="YES">
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47 <param name="masses" label="File of masses (Variable Metadata) " format="tabular" type="data" help="Generally variable metadata file. Please note : HMDB allows maximum 150 query masses per request" />
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48 <conditional name="header">
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49 <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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50 <option value="no">NO</option>
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51 <option value="yes" selected="true">YES</option>
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52 </param>
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53 <when value="yes">
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54 <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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55 </when>
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56 <when value="no"/>
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57 </conditional>
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58 <param name="colfactor" label="Column of masses " type="data_column" data_ref="masses" accept_default="true" />
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59 </when>
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60 <when value="NO">
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61 <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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62 </when>
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63 </conditional>
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64
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65 <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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66 <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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67 <param name="mode" label="Molecular Species " type="select" display="radio" help="">
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68 <option value="positive">Positif Mode</option>
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69 <option value="negative">Negatif Mode</option>
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70 <option value="neutral" selected="True">Neutral Mass</option>
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71 </param>
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72 </inputs>
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73
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74 <outputs>
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75 <data name="variableMetadata" format="tabular" label="${input_type.masses.name[:-6]}.HMDB.tabular">
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76 <filter>input_type['choice'] == "YES"</filter>
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77 </data>
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78 <data name="HmdbOutWeb" format="html" label="${input_type.masses.name[:-6]}.HMDB_WEB.html">
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79 <filter>input_type['choice'] == "YES"</filter>
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80 </data>
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81 <data name="HmdbOutXlsx" label="${input_type.masses.name[:-6]}.HMDB.xlsx" format="tabular">
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82 <filter>input_type['choice'] == "YES"</filter>
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83 </data>
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84 <data name="variableMetadata2" format="tabular" label="HMDB.tabular">
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85 <filter>input_type['choice'] == "NO"</filter>
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86 </data>
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87 <data name="HmdbOutWeb2" format="html" label="HMDB_WEB.html">
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88 <filter>input_type['choice'] == "NO"</filter>
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89 </data>
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90 <data name="HmdbOutXlsx2" label="HMDB.xlsx" format="tabular">
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91 <filter>input_type['choice'] == "NO"</filter>
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92 </data>
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93 </outputs>
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94
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95 <tests>
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96 <test>
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97 <!--test 01 no result - fake-mzrt-input-with-id -->
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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.xlsx"/>
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109 </test>
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110 <test>
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111 <!--test 02 : some results - with-mzrt-input-with-id file-->
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112 <param name="choice" value="YES"/>
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113 <param name="masses" value="input_test02_mzrt-input-with-id.tabular"/>
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114 <param name="header_choice" value="yes"/>
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115 <param name="nblineheader" value="1"/>
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116 <param name="colfactor" value="2"/>
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117 <param name="delta" value="0.001"/>
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118 <param name="mode" value="positive"/>
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119 <param name="maxquery" value="5"/>
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120 <output name="variableMetadata" file="out_test02.tabular"/>
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121 <output name="HmdbOutWeb" file="out_test02.html"/>
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122 <output name="HmdbOutXlsx" file="out_test02.xlsx"/>
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123 </test>
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124 <test>
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125 <!--test 03 : some results - with-mz list in manual mass mode-->
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126 <param name="choice" value="NO"/>
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127 <param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/>
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128 <param name="delta" value="0.05"/>
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129 <param name="mode" value="positive"/>
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130 <param name="maxquery" value="5"/>
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131 <output name="variableMetadata2" file="out_test03.tabular"/>
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132 <output name="HmdbOutWeb2" file="out_test03.html"/>
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133 <output name="HmdbOutXlsx2" file="out_test03.xlsx"/>
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134 </test>
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135 </tests>
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136
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137 <help><![CDATA[
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138
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139 .. class:: infomark
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140
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141 **Authors** Marion Landi and Franck Giacomoni
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142
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143 ---------------------------------------------------
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144
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145 .. class:: infomark
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146
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147 **Please cite** If you use this tool, please add the following reference
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148 | 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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149
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150
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151 ---------------------------------------------------
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152
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153 ==============
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154 HMDB MS search
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155 ==============
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156
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157 -----------
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158 Description
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159 -----------
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160
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161 | Search informations (like : HMDB id, Name, Adduct, delta mass) on HMDB online bank
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162 | with one or more mass(es) in a file or entered manually
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163
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164
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165 -----------------
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166 Workflow position
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167 -----------------
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168
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169
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170 .. image:: ./static/images/metabolomics/hmdb.png
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171 :width: 800
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172
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173
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174 -----------
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175 Input files
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176 -----------
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177
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178
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179 +-------------------------+-----------+
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180 | Parameter : num + label | Format |
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181 +=========================+===========+
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182 | 1 : File of masses | tabular |
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183 +-------------------------+-----------+
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184
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185 File of masses (Generally variable metadata file) must have at least the following column :
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186 * Masses : column with all the masses in the tsv input file
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187
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188 ----------
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189 Parameters
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190 ----------
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191
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192 Would you use a file
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193 | Choose whether the masses are in a file or entered manually
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194 | YES (default) : parameters **File of masses ; Do you have a header ; Column of masses** are visible
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195 | NO : parameter **Mass to submit** is visible
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196 |
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197
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198
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199 If 'use file'='YES'
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200
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201 File of masses
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202 | see "Input files" section above
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203 | Tabular file format, Generally variable metadata file
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204 |
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205
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206 Do you have a header
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207 | YES (default) : parameter **Number of header lines** is visible
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208 | NO : all lines are considered to contain masses
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209 |
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210
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211 If 'have a header'='YES'
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212
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213 Number of header lines
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214 | Number of lines not containing masses values, these lines will be ignored
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215 |
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216
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217 In all header cases :
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218
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219 Column of masses
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220 | Specify the column number for the mass in the tsv input file
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221 |
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222
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223
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224 If 'use file'='NO'
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225
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226 Mass to submit
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227 | Specify a list of mass to request
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228 | one or more mass(es) entered manually
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229 | For a masses list, writes : m1 m2 m3
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230 | You must separate yours values with space
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231 | dot (.) is for float number
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232 |
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233
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234 In all cases :
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235
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236 Mass-to-charge ratio
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237 | 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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238 |
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239
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240 Molecular Species
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241 | Type of ionization of the molecule : *positif, negatif, neutral*
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242 |
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243
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244
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245 ------------
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246 Output files
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247 ------------
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248
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249 Two types of files
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250 | HMDB_WEB.HTML: for viewing result via HTML.
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251 |
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252 | HMDB_TABULAR.tabular: for linking with others modules.
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253 |
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254 | HMDB_XLSX.xlsx: an excel-like output permitting manual annotation cleaning.
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255 |
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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 ---------------
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261 Working example
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262 ---------------
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263
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264
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265 .. class:: warningmark
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266
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267 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
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268 | Format Data For Postprocessing
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269 | Perform LCMS Annotations
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270
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271 .. class:: warningmark
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272
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273 And their "W4M courses 2015":
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274 | Using Galaxy4Metabolomics - W4M table format for Galaxy
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275 | Annotation Banks - Annotation
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276
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277
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278 ]]></help>
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279 </tool>