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1 <tool id="downloader_bank_hmdb" name="HMDB bank downloader" version="2018.12">
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2 <description>
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3 : get a specific metabolite bank (as Urine...) from HMDB web portal.
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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="6.15">perl-lwp-simple</requirement>
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9 <requirement type="package" version="6.15">perl-libwww-perl</requirement>
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10 <requirement type="package" version="1.74">perl-uri</requirement>
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11 <requirement type="package" version="1.97">perl-text-csv</requirement>
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12 <requirement type="package" version="3.52">perl-xml-twig</requirement>
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13 <requirement type="package" version="1.60">perl-archive-zip</requirement>
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14 <requirement type="package" version="2.064">perl-io-uncompress-gunzip</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 $__tool_directory__/downloader_bank_hmdb.pl
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24 -bank "$bank"
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25 -verbose "$verbose"
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26 -format "$bankformat"
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27 -outTab "$outTab"
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28
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29 ]]></command>
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30 <inputs>
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31 <param name="bank" type="select" label="What is the specific bank you want to download? " help="All banks are extracted from downloads section on HMDB web portal.">
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32 <option value="SERUM" selected="true">Human serum</option>
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33 <option value="URINE">Human urine</option>
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34 <option value="CSF">Human cerebrospinal fluid</option>
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35 <option value="FECES">Human feces</option>
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36 <option value="SALIVA">Human saliva</option>
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37 <option value="COW">Bovine</option>
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38 <option value="RUMEN">Bovine rumen</option>
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39 <option value="MILK">Bovine milk</option>
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40 </param>
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41 <param name="bankformat" type="select" label="Which output format do you need? " help="Proposed formats are lighter than downloaded raw files and adapted to annotation tools.">
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42 <option value="tabular" selected="true">tabular (for BiH tool)</option>
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43 <!--<option value="json">json (still in construction)</option>-->
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44 </param>
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45 <param name="verbose" type="select" label="Level of script verbose " help="Information about script running.">
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46 <option value="1" selected="true">low</option>
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47 <option value="3">high</option>
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48 </param>
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49 </inputs>
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50
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51 <outputs>
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52 <data name="outTab" format="tabular" label="REF_HMDB_${bank}.tabular"/>
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53 <!--<data name="outJson" format="json" label="REF_HMDB_${bank}.json"/>-->
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54 </outputs>
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55
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56 <tests>
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57 <test>
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58 <!--test 01 CSF download and produce a simple tabular -->
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59 <param name="bank" value="CSF"/>
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60 <param name="bankformat" value="tabular"/>
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61 <param name="verbose" value="1"/>
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62 <output name="outTab" file="out01.tabular"/>
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63 </test>
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64 </tests>
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65
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66 <help><![CDATA[
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67
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68 .. class:: infomark
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69
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70 **Authors** Charlotte Joly, Delphine Centeno and Franck Giacomoni
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71
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72 ---------------------------------------------------
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73
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74 .. class:: infomark
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75
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76 **Please cite** If you use this tool, please add the following reference
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77 | 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. Jan 4;46(D1):D608-17.
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78
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79
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80 ---------------------------------------------------
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81
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82 ====================
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83 HMDB bank downloader
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84 ====================
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85
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86 -----------
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87 Description
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88 -----------
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89
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90 | Download a bank containing information (like : HMDB id, Name, mz, inchikey)
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91 | from HMDB online web portal and convert it into W4M annotation tool input formats.
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92 |
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93
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94
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95 -----------------
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96 Workflow position
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97 -----------------
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98
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99
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100 .. image:: ./static/images/metabolomics/hmdb.png
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101 :width: 800
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102
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103
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104
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105 ----------
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106 Parameters
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107 ----------
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108
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109 What is the specific bank you want to download
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110 | Choose whether specific metabolite banks:
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111 | Urine
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112 | Serum
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113 | cerebrospinal fluid
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114 | ...
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115 |
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116
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117
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118 Which output format do you need
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119 | tabular : for W4M BiH annotation tool as example
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120 | json : still in construction
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121 |
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122
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123
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124
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125 ------------
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126 Output files
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127 ------------
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128
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129 Two types of files
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130 | REF_HMDB_BANKNAME.tabular: for W4M BiH annotation tool as example
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131 |
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132 | REF_HMDB_BANKNAME.json: for linking with others modules.
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133 |
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134
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135 ---------------------------------------------------
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136
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137
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138 ---------------
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139 Working example
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140 ---------------
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141
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142
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143 .. class:: warningmark
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144
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145 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
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146 | Format Data For Postprocessing
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147 | Perform LCMS Annotations
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148
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149 .. class:: warningmark
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150
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151 And their "W4M courses 2018":
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152 | Using Galaxy4Metabolomics - W4M table format for Galaxy
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153 | Annotation Banks - Annotation
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154
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155
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156 ]]></help>
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157 <!-- [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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158 <citations>
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159 <citation type="doi">10.1093/nar/gkx1089</citation>
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160 </citations>
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161 </tool> |
