Mercurial > repos > fgiacomoni > hmdb_ms_search
view wsdl_hmdb.xml @ 26:76872ac24fb2 draft
master branch Updating with tag :CI_COMMIT_TAG - - Fxx
| author | fgiacomoni |
|---|---|
| date | Wed, 27 Sep 2023 12:21:00 +0000 |
| parents | 8f7546d0b925 |
| children | 144e4a8ad000 |
line wrap: on
line source
<tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.3"> <description> search by masses on HMDB v5 online LCMS bank </description> <requirements> <requirement type="package" version="2.161">perl-data-dumper</requirement> <requirement type="package" version="2.97">perl-html-template</requirement> <requirement type="package" version="1.19">perl-soap-lite</requirement> <requirement type="package" version="6.15">perl-lwp-simple</requirement> <requirement type="package" version="6.15">perl-libwww-perl</requirement> <requirement type="package" version="1.74">perl-uri</requirement> <requirement type="package" version="1.97">perl-text-csv</requirement> <requirement type="package" version="3.52">perl-xml-twig</requirement> <requirement type="package" version="1.91">perl-www-mechanize</requirement> </requirements> <stdio> <exit_code range="1" level="fatal" /> </stdio> <command><![CDATA[ perl $__tool_directory__/wsdl_hmdb.pl #if str($input_type.choice) == "YES": -masses "${input_type.masses}" -header_choice "${input_type.header.header_choice}" #if str($input_type.header.header_choice) == "yes": -nblineheader "${$input_type.header.nbHeader}" #end if -colfactor "${input_type.colfactor}" -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xlsx "$HmdbOutXlsx" #else: -mass "${input_type.mass}" -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xlsx "$HmdbOutXlsx2" #end if -mode "${mode_type.mode}" #if str($mode_type.mode) == "positive": -adduct_type "${mode_type.data_positive_adducts}" #elif str($mode_type.mode) == "negative": -adduct_type "${mode_type.data_negative_adducts}" #elif str($mode_type.mode) == "neutral": -adduct_type "${mode_type.data_neutral_adducts}" #end if -delta "$delta" -maxquery "$maxquery" -advancedFeatures "$advancedFeatures" -verbose "$verbose" ]]></command> <inputs> <conditional name="input_type"> <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"> <option value="YES">YES</option> <option value="NO">NO</option> </param> <when value="YES"> <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" /> <conditional name="header"> <param name="header_choice" type="select" label="Do you have a header " help="if 'YES' is selected then enter your number of header lines"> <option value="no">NO</option> <option value="yes" selected="true">YES</option> </param> <when value="yes"> <param name="nbHeader" label="Number of header lines " type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/> </when> <when value="no"/> </conditional> <param name="colfactor" label="Column of masses " type="data_column" data_ref="masses" accept_default="true" /> </when> <when value="NO"> <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" /> </when> </conditional> <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)"/> <param name="maxquery" label="Number of maximum entries returned by the query " type="integer" value="10" min="1" max="50" size="10" help="Default value is 10 for each queried mz / max is 50"/> <conditional name="mode_type"> <param name="mode" label="Molecular Species " type="select" display="radio" help=""> <option value="positive">Positif Mode</option> <option value="negative">Negatif Mode</option> <option value="neutral" selected="True">Neutral Mass</option> </param> <when value="positive"> <param name="data_positive_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help=""> <option value="Unknown">Unknown</option> <option value="M+H" selected="True">M+H</option> <option value="M+H-2H2O">M+H-2H2O</option> <option value="M+H-H2O">M+H-H2O</option> <option value="M+NH4-H2O">M+NH4-H2O</option> <option value="M+Li">M+Li</option> <option value="M+NH4">M+NH4</option> <option value="M+Na">M+Na</option> <option value="M+CH3OH+H">M+CH3OH+H</option> <option value="M+K">M+K</option> <option value="M+ACN+H">M+ACN+H</option> <option value="M+2Na-H">M+2Na-H</option> <option value="M+IsoProp+H">M+IsoProp+H</option> <option value="M+ACN+Na">M+ACN+Na</option> <option value="M+2K-H">M+2K-H</option> <option value="M+DMSO+H">M+DMSO+H</option> <option value="M+2ACN+H">M+2ACN+H</option> <option value="M+IsoProp+Na+H">M+IsoProp+Na+H</option> <option value="M+H+HCOONa">M+H+HCOONa</option> <option value="2M+H">2M+H</option> <option value="2M+NH4">2M+NH4</option> <option value="2M+Na">2M+Na</option> <option value="2M+2H+3H2O">2M+2H+3H2O</option> <option value="2M+K">2M+K</option> <option value="2M+ACN+H">2M+ACN+H</option> <option value="2M+ACN+Na">2M+ACN+Na</option> <option value="2M+H-H2O">2M+H-H2O</option> <option value="M+2H">M+2H</option> <option value="M+H+NH4">M+H+NH4</option> <option value="M+H+Na">M+H+Na</option> <option value="M+H+K">M+H+K</option> <option value="M+ACN+2H">M+ACN+2H</option> <option value="M+2Na">M+2Na</option> <option value="M+2ACN+2H">M+2ACN+2H</option> <option value="M+3ACN+2H">M+3ACN+2H</option> <option value="M+3H">M+3H</option> <option value="M+2H+Na">M+2H+Na</option> <option value="M+H+2Na">M+H+2Na</option> <option value="M+3Na">M+3Na</option> <option value="M+H+2K">M+H+2K</option> </param> </when> <when value="negative"> <param name="data_negative_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help=""> <option value="Unknown">Unknown</option> <option value="M-H" selected="True">M-H</option> <option value="M-H20-H">M-H20-H</option> <option value="M+F">M+F</option> <option value="M+Na-2H">M+Na-2H</option> <option value="M+Cl">M+Cl</option> <option value="M+K-2H">M+K-2H</option> <option value="M+FA-H">M+FA-H</option> <option value="M+Hac-H">M+Hac-H</option> <option value="M+Br">M+Br</option> <option value="M+TFA-H">M+TFA-H</option> <option value="M-H+HCOONa">M-H+HCOONa</option> <option value="2M-H">2M-H</option> <option value="2M+FA-H">2M+FA-H</option> <option value="2M+Hac-H">2M+Hac-H</option> <option value="3M-H">3M-H</option> <option value="M-2H">M-2H</option> <option value="M-3H">M-3H</option> </param> </when> <when value="neutral"> <param name="data_neutral_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help=""> <option value="Unknown">Unknown</option> <option value="M" selected="True">M</option> </param> </when> </conditional> <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"> <option value="1">Advanced mode</option> <option value="0" selected="True">Default mode</option> </param> <param name="verbose" type="select" label="Verbose level" display="radio" help=""> <option value="1" selected="true">Low</option> <option value="3" >High</option> </param> </inputs> <outputs> <data name="variableMetadata" format="tabular" label="${input_type.masses.name[:-6]}.HMDB.tabular"> <filter>input_type['choice'] == "YES"</filter> </data> <data name="HmdbOutWeb" format="html" label="${input_type.masses.name[:-6]}.HMDB_WEB.html"> <filter>input_type['choice'] == "YES"</filter> </data> <data name="HmdbOutXlsx" label="${input_type.masses.name[:-6]}.HMDB_XLS.txt" format="tabular"> <filter>input_type['choice'] == "YES"</filter> </data> <data name="variableMetadata2" format="tabular" label="HMDB.tabular"> <filter>input_type['choice'] == "NO"</filter> </data> <data name="HmdbOutWeb2" format="html" label="HMDB_WEB.html"> <filter>input_type['choice'] == "NO"</filter> </data> <data name="HmdbOutXlsx2" label="HMDB_XLS.txt" format="tabular"> <filter>input_type['choice'] == "NO"</filter> </data> </outputs> <tests> <!--test 01 no result - fake-mzrt-input-with-id --> <!-- <test> <param name="choice" value="YES"/> <param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/> <param name="header_choice" value="yes"/> <param name="nblineheader" value="1"/> <param name="colfactor" value="2"/> <param name="delta" value="0.001"/> <param name="mode" value="neutral"/> <param name="maxquery" value="5"/> <output name="variableMetadata" file="out_test01.tabular"/> <output name="HmdbOutWeb" file="out_test01.html"/> <output name="HmdbOutXlsx" file="out_test01.txt"/> </test> --> <!--test 02 : some results - with-mzrt-input-with-id file--> <!-- <test> <param name="choice" value="YES"/> <param name="masses" value="input_test02_mzrt-input-with-id.tabular"/> <param name="header_choice" value="yes"/> <param name="nblineheader" value="1"/> <param name="colfactor" value="2"/> <param name="delta" value="0.001"/> <param name="mode" value="positive"/> <param name="maxquery" value="5"/> <output name="variableMetadata" file="out_test02.tabular"/> <output name="HmdbOutWeb" file="out_test02.html"/> <output name="HmdbOutXlsx" file="out_test02.txt"/> </test> --> <!--test 03 : some results - with-mz list in manual mass mode--> <test> <param name="choice" value="NO"/> <param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/> <param name="delta" value="0.05"/> <param name="mode" value="positive"/> <param name="maxquery" value="5"/> <param name="data_positive_adducts" value="M+H"/> <output name="variableMetadata2" file="out_test03.tabular"/> <output name="HmdbOutWeb2" file="out_test03.html"/> <output name="HmdbOutXlsx2" file="out_test03.txt"/> </test> </tests> <help><![CDATA[ .. class:: infomark **Authors** Marion Landi, Yann Guitton and Franck Giacomoni --------------------------------------------------- .. class:: infomark **Please cite** If you use this tool, please add the following reference | 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. | 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. | Wishart DS et al, HMDB 5.0 - the Human Metabolome Database for 2022, Nucleic Acids Res. 2022. --------------------------------------------------- ============== HMDB MS search ============== ----------- Description ----------- | Search informations (like : HMDB id, Name, Adduct, delta mass) on HMDB online bank | with one or more mass(es) in a file or entered manually ----------------- Workflow position ----------------- .. image:: ./static/images/metabolomics/hmdb.png :width: 800 ----------- Input files ----------- +-------------------------+-----------+ | Parameter : num + label | Format | +=========================+===========+ | 1 : File of masses | tabular | +-------------------------+-----------+ File of masses (Generally variable metadata file) must have at least the following column : * Masses : column with all the masses in the tsv input file ---------- Parameters ---------- Would you use a file | Choose whether the masses are in a file or entered manually | YES (default) : parameters **File of masses ; Do you have a header ; Column of masses** are visible | NO : parameter **Mass to submit** is visible | If 'use file'='YES' File of masses | see "Input files" section above | Tabular file format, Generally variable metadata file | Do you have a header | YES (default) : parameter **Number of header lines** is visible | NO : all lines are considered to contain masses | If 'have a header'='YES' Number of header lines | Number of lines not containing masses values, these lines will be ignored | In all header cases : Column of masses | Specify the column number for the mass in the tsv input file | If 'use file'='NO' Mass to submit | Specify a list of mass to request | one or more mass(es) entered manually | For a masses list, writes : m1 m2 m3 | You must separate yours values with space | dot (.) is for float number | In all cases : Mass-to-charge ratio | Specify a delta (mass-to-charge ratio) to apply on mass - This value is a float, between 0.0000000000000001 and 10. | Molecular Species | Type of ionization of the molecule : *positif, negatif, neutral* | ------------ Output files ------------ Two types of files | HMDB_WEB.HTML: for viewing result via HTML. | | HMDB_TABULAR.tabular: for linking with others modules. | | HMDB_XLS.txt: an excel-like output permitting manual annotation cleaning. | --------------------------------------------------- --------------- Working example --------------- .. class:: warningmark Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto | Format Data For Postprocessing | Perform LCMS Annotations .. class:: warningmark And their "W4M courses 2022": | Using Galaxy4Metabolomics - W4M table format for Galaxy | Annotation Banks - Annotation ]]></help> <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel --> <citations> <citation type="doi">10.1093/nar/gks1065</citation> <citation type="doi">10.1093/nar/gkx1089</citation> <citation type="doi">10.1093/nar/gkab1062</citation> </citations> </tool>