Mercurial > repos > fgiacomoni > downloader_bank_hmdb
annotate downloader_bank_hmdb.xml @ 2:be504ccbc41c draft default tip
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| author | fgiacomoni |
|---|---|
| date | Wed, 30 Nov 2022 16:14:27 +0000 |
| parents | 7c9269bded0e |
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| rev | line source |
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1 <tool id="downloader_bank_hmdb" name="Wishart bank downloader" version="1.1.2"> |
| 0 | 2 <description> |
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3 : get a specific metabolite bank (as Urine, Serum...) from Wishart web portal. |
| 0 | 4 </description> |
| 5 | |
| 6 <requirements> | |
| 7 <requirement type="package" version="2.161">perl-data-dumper</requirement> | |
| 8 <requirement type="package" version="6.15">perl-lwp-simple</requirement> | |
| 9 <requirement type="package" version="6.15">perl-libwww-perl</requirement> | |
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10 <requirement type="package" version="6.07">perl-lwp-protocol-https</requirement> |
| 0 | 11 <requirement type="package" version="1.74">perl-uri</requirement> |
| 12 <requirement type="package" version="1.97">perl-text-csv</requirement> | |
| 13 <requirement type="package" version="3.52">perl-xml-twig</requirement> | |
| 14 <requirement type="package" version="1.60">perl-archive-zip</requirement> | |
| 15 <requirement type="package" version="2.064">perl-io-uncompress-gunzip</requirement> | |
| 16 </requirements> | |
| 17 | |
| 18 <stdio> | |
| 19 <exit_code range="1" level="fatal" /> | |
| 20 </stdio> | |
| 21 | |
| 22 | |
| 23 <command><![CDATA[ | |
| 24 perl $__tool_directory__/downloader_bank_hmdb.pl | |
| 25 -bank "$bank" | |
| 26 -verbose "$verbose" | |
| 27 -format "$bankformat" | |
| 28 -outTab "$outTab" | |
| 29 | |
| 30 ]]></command> | |
| 31 <inputs> | |
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32 <param name="bank" type="select" label="What is the specific bank you want to download? " help="All banks are extracted from downloads section on Whishart web portals."> |
| 0 | 33 <option value="SERUM" selected="true">Human serum</option> |
| 34 <option value="URINE">Human urine</option> | |
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35 <option value="SWEAT">Human sweat</option> |
| 0 | 36 <option value="CSF">Human cerebrospinal fluid</option> |
| 37 <option value="FECES">Human feces</option> | |
| 38 <option value="SALIVA">Human saliva</option> | |
| 39 <option value="COW">Bovine</option> | |
| 40 <option value="MILK">Bovine milk</option> | |
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41 <option value="TOXIC">Toxin and Toxin Target Database</option> |
| 0 | 42 </param> |
| 43 <param name="bankformat" type="select" label="Which output format do you need? " help="Proposed formats are lighter than downloaded raw files and adapted to annotation tools."> | |
| 44 <option value="tabular" selected="true">tabular (for BiH tool)</option> | |
| 45 <!--<option value="json">json (still in construction)</option>--> | |
| 46 </param> | |
| 47 <param name="verbose" type="select" label="Level of script verbose " help="Information about script running."> | |
| 48 <option value="1" selected="true">low</option> | |
| 49 <option value="3">high</option> | |
| 50 </param> | |
| 51 </inputs> | |
| 52 | |
| 53 <outputs> | |
| 54 <data name="outTab" format="tabular" label="REF_HMDB_${bank}.tabular"/> | |
| 55 <!--<data name="outJson" format="json" label="REF_HMDB_${bank}.json"/>--> | |
| 56 </outputs> | |
| 57 | |
| 58 <tests> | |
| 59 <test> | |
| 60 <!--test 01 CSF download and produce a simple tabular --> | |
| 61 <param name="bank" value="CSF"/> | |
| 62 <param name="bankformat" value="tabular"/> | |
| 63 <param name="verbose" value="1"/> | |
| 64 <output name="outTab" file="out01.tabular"/> | |
| 65 </test> | |
| 66 </tests> | |
| 67 | |
| 68 <help><![CDATA[ | |
| 69 | |
| 70 .. class:: infomark | |
| 71 | |
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72 **Authors** Charlotte Joly, Delphine Centeno, Lain Pavot, Yann Guitton and Franck Giacomoni |
| 0 | 73 |
| 74 --------------------------------------------------- | |
| 75 | |
| 76 .. class:: infomark | |
| 77 | |
| 78 **Please cite** If you use this tool, please add the following reference | |
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79 | Wishart DS, Guo AC, Oler E, et al., HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Res. 2022. Jan 7;50(D1):D622–31. |
| 0 | 80 |
| 81 | |
| 82 --------------------------------------------------- | |
| 83 | |
| 84 ==================== | |
| 85 HMDB bank downloader | |
| 86 ==================== | |
| 87 | |
| 88 ----------- | |
| 89 Description | |
| 90 ----------- | |
| 91 | |
| 92 | Download a bank containing information (like : HMDB id, Name, mz, inchikey) | |
| 93 | from HMDB online web portal and convert it into W4M annotation tool input formats. | |
| 94 | | |
| 95 | |
| 96 | |
| 97 ----------------- | |
| 98 Workflow position | |
| 99 ----------------- | |
| 100 | |
| 101 | |
| 102 .. image:: ./static/images/metabolomics/hmdb.png | |
| 103 :width: 800 | |
| 104 | |
| 105 | |
| 106 | |
| 107 ---------- | |
| 108 Parameters | |
| 109 ---------- | |
| 110 | |
| 111 What is the specific bank you want to download | |
| 112 | Choose whether specific metabolite banks: | |
| 113 | Urine | |
| 114 | Serum | |
| 115 | cerebrospinal fluid | |
| 116 | ... | |
| 117 | | |
| 118 | |
| 119 | |
| 120 Which output format do you need | |
| 121 | tabular : for W4M BiH annotation tool as example | |
| 122 | json : still in construction | |
| 123 | | |
| 124 | |
| 125 | |
| 126 | |
| 127 ------------ | |
| 128 Output files | |
| 129 ------------ | |
| 130 | |
| 131 Two types of files | |
| 132 | REF_HMDB_BANKNAME.tabular: for W4M BiH annotation tool as example | |
| 133 | | |
| 134 | |
| 135 --------------------------------------------------- | |
| 136 | |
| 137 | |
| 138 --------------- | |
| 139 Working example | |
| 140 --------------- | |
| 141 | |
| 142 | |
| 143 .. class:: warningmark | |
| 144 | |
| 145 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto | |
| 146 | Format Data For Postprocessing | |
| 147 | Perform LCMS Annotations | |
| 148 | |
| 149 .. class:: warningmark | |
| 150 | |
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151 And their "W4M courses 2020": |
| 0 | 152 | Using Galaxy4Metabolomics - W4M table format for Galaxy |
| 153 | Annotation Banks - Annotation | |
| 154 | |
| 155 | |
| 156 ]]></help> | |
| 157 <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel --> | |
| 158 <citations> | |
| 159 <citation type="doi">10.1093/nar/gkx1089</citation> | |
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160 <citation type="doi">10.1093/nar/gku1004</citation> |
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161 <citation type="doi">10.1093/nar/gkab1062</citation> |
| 0 | 162 </citations> |
| 163 </tool> |