Mercurial > repos > fgiacomoni > hmdb_ms_search
view hmdb/wsdl_hmdb.xml @ 0:9583f9772198 draft
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author | fgiacomoni |
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date | Thu, 28 Jan 2016 10:52:26 -0500 |
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<tool id="wsdl_hmdb" name="HMDB MS search" version="2016-01-28"> <description> search by masses on HMDB online bank </description> <command interpreter="perl"> 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 "${input_type.colfactor}" #else: -mass "${input_type.mass}" #end if -delta "$delta" -mode "$mode" -output "$variableMetadata" -view "$HmdbResView" -outputxls "$HmdbResXls" </command> <inputs> <conditional name="input_type"> <param name="choice" type="select" label="Would you use a file " help="if 'NO' is selected then one or more mass(es) must be entered manually"> <option value="YES">YES</option> <option value="NO">NO</option> </param> <when value="YES"> <param name="masses" label="File of masses (Variable Metadata) " format="tabular" type="data" help="Generally variable metadata file. Please note : HMDB allows maximum 150 query masses per request" /> <conditional name="header"> <param name="header_choice" type="select" label="Do you have a header " help="if 'YES' is selected then enter your number of header lines"> <option value="no">NO</option> <option value="yes" selected="true">YES</option> </param> <when value="yes"> <param name="nbHeader" label="Number of header lines " type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/> </when> </conditional> <param name="colfactor" label="Column of masses " type="data_column" data_ref="masses" accept_default="true" /> </when> <when value="NO"> <param name="mass" label="Mass to submit " type="text" size="20" help="For a masses list, writes : m1 m2 m3. Your values must be separated by spaces. You should use dot (.) like decimal separator" /> </when> </conditional> <param name="delta" label="Mass-to-charge ratio " type="float" value="0.05" min="0" max="10" size="10" help="Default value is 0.05 for HMDB (mass-to-charge ratio)"/> <param name="mode" label="Molecular Species " type="select" display="radio" help=""> <option value="positive">Positif Mode</option> <option value="negative">Negatif Mode</option> <option value="neutral" selected="True">Neutral Mass</option> </param> </inputs> <outputs> <data name="variableMetadata" format="tabular" label="${tool.name}_TSV"/> <data name="HmdbResView" format="html" label="${tool.name}_VIEW"/> <data name="HmdbResXls" label="${tool.name}_XLS" format="tabular" /> </outputs> <tests> <test> <!--test 01 no result - fake-mzrt-input-with-id --> <param name="choice" value="YES"/> <param name="masses" value="input_test01_fake-mzrt-input-with-id.tsv"/> <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"/> <output name="variableMetadata" file="out_test01.tsv"/> <output name="HmdbResView" file="out_test01.html"/> <output name="HmdbResXls" file="out_test01.csv"/> </test> <test> <!--test 02 : some results - with-mzrt-input-with-id file--> <param name="choice" value="YES"/> <param name="masses" value="input_test02_mzrt-input-with-id.tsv"/> <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"/> <output name="variableMetadata" file="out_test02.tsv"/> <output name="HmdbResView" file="out_test02.html"/> <output name="HmdbResXls" file="out_test02.csv"/> </test> <test> <!--test 03 : some results - with-mz list in manual mass mode--> <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"/> <output name="variableMetadata" file="out_test03.tsv"/> <output name="HmdbResView" file="out_test03.html"/> <output name="HmdbResXls" file="out_test03.csv"/> </test> </tests> <help> .. class:: infomark **Authors** Marion Landi and Franck Giacomoni --------------------------------------------------- .. class:: infomark **Please cite** If you use this tool, please cite | `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. <http://www.ncbi.nlm.nih.gov/pubmed/23161693>`_ --------------------------------------------------- ============== 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 | wsdl_hmdb_VIEW.HTML : for viewing result via HTML. | | wsdl_hmdb_TSV.tabular : for linking with others modules. | | an excel-like output will be available. | --------------------------------------------------- --------------- Working example --------------- .. class:: warningmark Refer to the corresponding `"W4M HowTo" <http://workflow4metabolomics.org/howto>`_ page: | Format Data For Postprocessing | Perform LCMS Annotations .. class:: warningmark And their "W4M courses 2015": | Using Galaxy4Metabolomics - W4M table format for Galaxy | Annotation Banks - Annotation </help> </tool>