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view wsdl_lipidmaps.xml @ 2:1276908e8fc4 draft
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| author | fgiacomoni |
|---|---|
| date | Mon, 20 Aug 2018 09:17:05 -0400 |
| parents | e8bd49794291 |
| children | f4e6b77c46e3 |
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<tool id="lipidmaps" name="Lipidmaps " version="2018-08-20"> <description> : search on LIPID MAPS Structure Database (LMSD) online with masses and its Text/Ontology-based search engine. </description> <requirements> <requirement type="package" version="0.413">perl-list-moreutils</requirement> <requirement type="package" version="1.33">perl-text-csv</requirement> <requirement type="package" version="2.95">perl-html-template</requirement> <requirement type="package" version="3.49">perl-xml-twig</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="1.9728">perl-time-hires</requirement> </requirements> <stdio> <exit_code level="fatal" range="1"/> </stdio> <command><![CDATA[ perl $__tool_directory__/wsdl_lipidmaps.pl -input $file_input -lineheader $lineheader -colmass $col_mass -decimal $decimal -round $round_type -delta $tolerance -mode $mode #if str($query_type.complex_query_action) == "no" : -cat "${query_type.select_cat.filter_cat}" -class "${query_type.select_cat.select_class.filter_class}" -subclass "${query_type.select_cat.select_class.select_subclass.filter_subclass}" #else : -colclassif "${query_type.col_classif_id}" #end if #if str($data_type.modify_data_action) == "yes" : -listneutralloss ${data_type.neutral_loss} -listoxidation ${data_type.oxidation} #end if -output $variableMetadata_out -view $LMSDOutWeb -summary $LMSDOutSum ]]></command> <inputs> <param name="file_input" label="File of masses (Variable Metadata) " format="tabular" type="data" help="A tabular/csv file is needed and can contains a header line."/> <param name="lineheader" label="Number of header lines " type="integer" value="0" size="10" help="number of lines not containing values"/> <param name="col_mass" label="Masses Column " type="data_column" data_ref="file_input" accept_default="true" help="select the column in your input file."/> <param name="mode" label="Ionisation mode of your submitted data " type="select" help="Please be aware !!! This service of LipidMaps uses Neutral mass - If you need to transform your masses for the query, please select the ionisation mode (positive or negative) of your instrument- This operation is really pertinent only if yours masses corresponding to [M+H]+ or [M-H]- species"> <option value="POS">Positive</option> <option value="NEG">Negative</option> <option value="NEU" selected="True">Neutral</option> </param> <!--<param name="col_rt" label="Retention time Column " type="data_column" data_ref="file_input" accept_default="true" help="select the column in your input file."/>--> <conditional name="data_type"> <param name="modify_data_action" label="Do you want to modify input masses ? " type="select" help="Posibility to apply oxidation(s) and/or neutral loss(es)."> <option value="yes">yes</option> <option value="no" selected="True">no</option> </param> <when value="no"/> <when value="yes"> <!-- Part to update with list of compound oxidation --> <param name="oxidation" type="select" display="checkboxes" multiple="True" label="If you want to transform masses extracted from file with oxidation(s) " help="Select one or more boxes"> <option value="NA" selected="True">No oxidation</option> <option value="loss_O">+ O</option> <option value="loss_2O">+ 2 O</option> <option value="loss_4O">+ 4 O</option> </param> <!-- Part to update with list of compound oxidation --> <!-- Part to update with list of neutral_loss --> <param name="neutral_loss" type="select" display="checkboxes" multiple="True" label="If you want to correct masses extracted from file with neutral loss " help="Select one or more boxes"> <option value="NA" selected="True">No neutral loss</option> <option value="loss_hydroperoxide">H2O2 loss</option> <option value="loss_water">H2O loss</option> </param> <!-- Part to update with list of neutral_loss --> </when> </conditional> <!-- Query type : simple or multiple --> <conditional name="query_type"> <param name="complex_query_action" label="Do you want to perform a multiple queries on input masses ? " type="select" help="Choose 'no' to use the following classification on all mz or 'yes' to search each mz on one given cat/class/subclass. "> <option value="yes">yes</option> <option value="no" selected="True">no</option> </param> <when value="yes"> <param name="col_classif_id" label="Select the column containing category or class or sub class identifiants in your input file : " type="data_column" data_ref="file_input" accept_default="true" help="Example : 3 for Glycerophospholipids category, 310 for Glycerophosphates main class or 32001 for a subclass "/> </when> <when value="no"> <!-- Part to update with new LIPIDMAPS Tax --> <conditional name="select_cat"> <param name="filter_cat" label="Select a Lipid category for your query " type="select"> <option value="1">Fatty Acyls [FA]</option> <option value="2">Glycerolipids [GL]</option> <option value="3">Glycerophospholipids [GP]</option> <option value="4">Sphingolipids [SP]</option> <option value="5">Sterol Lipids [ST]</option> <option value="6">Prenol Lipids [PR]</option> <option value="7">Saccharolipids [SL]</option> <option value="8">Polyketides [PK]</option> <option value="NA_0" selected="True">No category selected</option> </param> <when value="NA_0"> <conditional name="select_class"> <param name="filter_class" label="Select a Lipid main class for your query " type="select"> <option value="NA_1">No main class selected</option> </param> <when value="NA_1"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_100">No subclass available</option> </param> <when value="NA_100"></when> </conditional> </when> </conditional> </when> <when value="1"> <conditional name="select_class"> <param name="filter_class" label="Select a Lipid main class for your query " type="select"> <option value="101">Fatty Acids and Conjugates [FA01]</option> <option value="102">Octadecanoids [FA02]</option> <option value="103">Eicosanoids [FA03]</option> <option value="104">Docosanoids [FA04]</option> <option value="105">Fatty alcohols [FA05]</option> <option value="106">Fatty aldehydes [FA06]</option> <option value="107">Fatty esters [FA07]</option> <option value="108">Fatty amides [FA08]</option> <option value="109">Fatty nitriles [FA09]</option> <option value="110">Fatty ethers [FA10]</option> <option value="111">Hydrocarbons [FA11]</option> <option value="112">Oxygenated hydrocarbons [FA12]</option> <option value="113">Fatty acyl glycosides [FA13]</option> <option value="100">Other Fatty Acyls [FA00]</option> <option value="NA_1" selected="True">No main class selected</option> </param> <when value="NA_1"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_100">No subclass available</option> </param> <when value="NA_100"></when> </conditional> </when> <when value="101"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="10101">Straight chain fatty acids [FA0101]</option> <option value="10102">Branched fatty acids [FA0102]</option> <option value="10103">Unsaturated fatty acids [FA0103]</option> <option value="10104">Hydroperoxy fatty acids [FA0104]</option> <option value="10105">Hydroxy fatty acids [FA0105]</option> <option value="10106">Oxo fatty acids [FA0106]</option> <option value="10107">Epoxy fatty acids [FA0107]</option> <option value="10108">Methoxy fatty acids [FA0108]</option> <option value="10109">Halogenated fatty acids [FA0109]</option> <option value="10110">Amino fatty acids [FA0110]</option> <option value="10111">Cyano fatty acids [FA0111]</option> <option value="10112">Nitro fatty acids [FA0112]</option> <option value="10113">Thia fatty acids [FA0113]</option> <option value="10114">Carbocyclic fatty acids [FA0114]</option> <option value="10115">Heterocyclic fatty acids [FA0115]</option> <option value="10116">Mycolic acids [FA0116]</option> <option value="10117">Dicarboxylic acids [FA0117]</option> <option value="NA_101" selected="True">No subclass selected</option> </param> <when value="NA_101"></when> <when value="10101"></when> <when value="10102"></when> <when value="10103"></when> <when value="10104"></when> <when value="10105"></when> <when value="10106"></when> <when value="10107"></when> <when value="10108"></when> <when value="10109"></when> <when value="10110"></when> <when value="10111"></when> <when value="10112"></when> <when value="10113"></when> <when value="10114"></when> <when value="10115"></when> <when value="10116"></when> <when value="10117"></when> </conditional> </when> <when value="102"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="10201">12-oxophytodienoic acid metabolites [FA0201]</option> <option value="10202">Jasmonic acids [FA0202]</option> <option value="10200">Other Octadecanoids [FA0200]</option> <option value="NA_102" selected="True">No subclass selected</option> </param> <when value="NA_102"></when> <when value="10201"></when> <when value="10202"></when> <when value="10200"></when> </conditional> </when> <when value="103"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="10301">Prostaglandins [FA0301]</option> <option value="10302">Leukotrienes [FA0302]</option> <option value="10303">Thromboxanes [FA0303]</option> <option value="10304">Lipoxins [FA0304]</option> <option value="10305">Hydroxy/hydroperoxyeicosatrienoic acids [FA0305]</option> <option value="10306">Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306]</option> <option value="10307">Hydroxy/hydroperoxyeicosapentaenoic acids [FA0307]</option> <option value="10308">Epoxyeicosatrienoic acids [FA0308]</option> <option value="10309">Hepoxilins [FA0309]</option> <option value="10310">Levuglandins [FA0310]</option> <option value="10311">Isoprostanes [FA0311]</option> <option value="10312">Clavulones and derivatives [FA0312]</option> <option value="10300">Other Eicosanoids [FA0300]</option> <option value="NA_103" selected="True">No subclass selected</option> </param> <when value="NA_103"></when> <when value="10301"></when> <when value="10302"></when> <when value="10303"></when> <when value="10304"></when> <when value="10305"></when> <when value="10306"></when> <when value="10307"></when> <when value="10308"></when> <when value="10309"></when> <when value="10310"></when> <when value="10311"></when> <when value="10312"></when> <when value="10300"></when> </conditional> </when> <when value="104"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_104">No subclass available</option> </param> <when value="NA_104"></when> </conditional> </when> <when value="105"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_105">No subclass available</option> </param> <when value="NA_105"></when> </conditional> </when> <when value="106"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_106">No subclass available</option> </param> <when value="NA_106"></when> </conditional> </when> <when value="107"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="10701">Wax monoesters [FA0701]</option> <option value="10702">Wax diesters [FA0702]</option> <option value="10703">Cyano esters [FA0703]</option> <option value="10704">Lactones [FA0704]</option> <option value="10705">Fatty acyl CoAs [FA0705]</option> <option value="10706">Fatty acyl ACPs [FA0706]</option> <option value="10707">Fatty acyl carnitines [FA0707]</option> <option value="10708">Fatty acyl adenylates [FA0708]</option> <option value="NA_107" selected="True">No subclass selected</option> </param> <when value="NA_107"></when> <when value="10701"></when> <when value="10702"></when> <when value="10703"></when> <when value="10704"></when> <when value="10705"></when> <when value="10706"></when> <when value="10707"></when> <when value="10708"></when> </conditional> </when> <when value="108"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="10801">Primary amides [FA0801]</option> <option value="10802">N-acyl amines [FA0802]</option> <option value="10803">Fatty acyl homoserine lactones [FA0803]</option> <option value="10804">N-acyl ethanolamines (endocannabinoids) [FA0804]</option> <option value="NA_108" selected="True">No subclass selected</option> </param> <when value="NA_108"></when> <when value="10801"></when> <when value="10802"></when> <when value="10803"></when> <when value="10804"></when> </conditional> </when> <when value="109"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_109">No subclass available</option> </param> <when value="NA_109"></when> </conditional> </when> <when value="110"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_110">No subclass available</option> </param> <when value="NA_110"></when> </conditional> </when> <when value="111"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_111">No subclass available</option> </param> <when value="NA_111"></when> </conditional> </when> <when value="112"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_112">No subclass available</option> </param> <when value="NA_112"></when> </conditional> </when> <when value="113"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="11301">Fatty acyl glycosides of mono- and disaccharides [FA1301]</option> <option value="11302">Sophorolipids [FA1302]</option> <option value="11303">Rhamnolipids [FA1303]</option> <option value="11300">Other Fatty acyl glycosides [FA1300]</option> <option value="NA_113" selected="True">No subclass selected</option> </param> <when value="NA_113"></when> <when value="11301"></when> <when value="11302"></when> <when value="11303"></when> <when value="11300"></when> </conditional> </when> <when value="100"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_100">No subclass available</option> </param> <when value="NA_100"></when> </conditional> </when> </conditional> </when> <when value="2"> <conditional name="select_class"> <param name="filter_class" label="Select a Lipid main class for your query " type="select"> <option value="201">Monoradylglycerols [GL01]</option> <option value="202">Diradylglycerols [GL02]</option> <option value="203">Triradylglycerols [GL03]</option> <option value="204">Glycosylmonoradylglycerols [GL04]</option> <option value="205">Glycosyldiradylglycerols [GL05]</option> <option value="200">Other Glycerolipids [GL00]</option> <option value="NA_2" selected="True">No main class selected</option> </param> <when value="NA_2"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_200">No subclass available</option> </param> <when value="NA_200"></when> </conditional> </when> <when value="201"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="20101">Monoacylglycerols [GL0101]</option> <option value="20102">Monoalkylglycerols [GL0102]</option> <option value="20103">Mono-(1Z-alkenyl)-glycerols [GL0103]</option> <option value="NA_201" selected="True">No subclass selected</option> </param> <when value="NA_201"></when> <when value="20101"></when> <when value="20102"></when> <when value="20103"></when> </conditional> </when> <when value="202"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="20201">Diacylglycerols [GL0201]</option> <option value="20202">1-alkyl,2-acylglycerols [GL0202]</option> <option value="20207">1-acyl,2-alkylglycerols [GL0207]</option> <option value="20203">Dialkylglycerols [GL0203]</option> <option value="20204">1Z-alkenylacylglycerols [GL0204]</option> <option value="20205">Di-glycerol tetraethers [GL0205]</option> <option value="20206">Di-glycerol tetraether glycans [GL0206]</option> <option value="NA_202" selected="True">No subclass selected</option> </param> <when value="NA_202"></when> <when value="20201"></when> <when value="20202"></when> <when value="20207"></when> <when value="20203"></when> <when value="20204"></when> <when value="20205"></when> <when value="20206"></when> </conditional> </when> <when value="203"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="20301">Triacylglycerols [GL0301]</option> <option value="20302">Alkyldiacylglycerols [GL0302]</option> <option value="20303">Dialkylmonoacylglycerols [GL0303]</option> <option value="20304">1Z-alkenyldiacylglycerols [GL0304]</option> <option value="20305">Estolides [GL0305]</option> <option value="NA_203" selected="True">No subclass selected</option> </param> <when value="NA_203"></when> <when value="20301"></when> <when value="20302"></when> <when value="20303"></when> <when value="20304"></when> <when value="20305"></when> </conditional> </when> <when value="204"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="20401">Glycosylmonoacylglycerols [GL0401]</option> <option value="20402">Glycosylmonoalkylglycerols [GL0402]</option> <option value="NA_204" selected="True">No subclass selected</option> </param> <when value="NA_204"></when> <when value="20401"></when> <when value="20402"></when> </conditional> </when> <when value="205"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="20501">Glycosyldiacylglycerols [GL0501]</option> <option value="20502">Glycosylalkylacylglycerols [GL0502]</option> <option value="20503">Glycosyldialkylglycerols [GL0503]</option> <option value="NA_205" selected="True">No subclass selected</option> </param> <when value="NA_205"></when> <when value="20501"></when> <when value="20502"></when> <when value="20503"></when> </conditional> </when> <when value="200"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_200">No subclass available</option> </param> <when value="NA_200"></when> </conditional> </when> </conditional> </when> <when value="3"> <conditional name="select_class"> <param name="filter_class" label="Select a Lipid main class for your query " type="select"> <option value="301">Glycerophosphocholines [GP01]</option> <option value="302">Glycerophosphoethanolamines [GP02]</option> <option value="303">Glycerophosphoserines [GP03]</option> <option value="304">Glycerophosphoglycerols [GP04]</option> <option value="305">Glycerophosphoglycerophosphates [GP05]</option> <option value="306">Glycerophosphoinositols [GP06]</option> <option value="307">Glycerophosphoinositol monophosphates [GP07]</option> <option value="308">Glycerophosphoinositol bisphosphates [GP08]</option> <option value="309">Glycerophosphoinositol trisphosphates [GP09]</option> <option value="310">Glycerophosphates [GP10]</option> <option value="311">Glyceropyrophosphates [GP11]</option> <option value="312">Glycerophosphoglycerophosphoglycerols [GP12]</option> <option value="313">CDP-Glycerols [GP13]</option> <option value="314">Glycosylglycerophospholipids [GP14]</option> <option value="315">Glycerophosphoinositolglycans [GP15]</option> <option value="316">Glycerophosphonocholines [GP16]</option> <option value="317">Glycerophosphonoethanolamines [GP17]</option> <option value="318">Di-glycerol tetraether phospholipids (caldarchaeols) [GP18]</option> <option value="319">Glycerol-nonitol tetraether phospholipids [GP19]</option> <option value="320">Oxidized glycerophospholipids [GP20]</option> <option value="300">Other Glycerophospholipids [GP00]</option> <option value="NA_3" selected="True">No main class selected</option> </param> <when value="NA_3"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_300">No subclass available</option> </param> <when value="NA_300"></when> </conditional> </when> <when value="301"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="30101">Diacylglycerophosphocholines [GP0101]</option> <option value="30102">1-alkyl,2-acylglycerophosphocholines [GP0102]</option> <option value="30108">1-acyl,2-alkylglycerophosphocholines [GP0108]</option> <option value="30103">1-(1Z-alkenyl),2-acylglycerophosphocholines [GP0103]</option> <option value="30109">1-acyl,2-(1Z-alkenyl)-glycerophosphocholines [GP0109]</option> <option value="30104">Dialkylglycerophosphocholines [GP0104]</option> <option value="30105">Monoacylglycerophosphocholines [GP0105]</option> <option value="30106">Monoalkylglycerophosphocholines [GP0106]</option> <option value="30107">1Z-alkenylglycerophosphocholines [GP0107]</option> <option value="NA_301" selected="True">No subclass selected</option> </param> <when value="NA_301"></when> <when value="30101"></when> <when value="30102"></when> <when value="30108"></when> <when value="30103"></when> <when value="30109"></when> <when value="30104"></when> <when value="30105"></when> <when value="30106"></when> <when value="30107"></when> </conditional> </when> <when value="302"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="30201">Diacylglycerophosphoethanolamines [GP0201]</option> <option value="30202">1-alkyl,2-acylglycerophosphoethanolamines [GP0202]</option> <option value="30208">1-acyl,2-alkylglycerophosphoethanolamines [GP0208]</option> <option value="30203">1-(1Z-alkenyl),2-acylglycerophosphoethanolamines [GP0203]</option> <option value="30204">Dialkylglycerophosphoethanolamines [GP0204]</option> <option value="30205">Monoacylglycerophosphoethanolamines [GP0205]</option> <option value="30206">Monoalkylglycerophosphoethanolamines [GP0206]</option> <option value="30207">1Z-alkenylglycerophosphoethanolamines [GP0207]</option> <option value="NA_302" selected="True">No subclass selected</option> </param> <when value="NA_302"></when> <when value="30201"></when> <when value="30202"></when> <when value="30208"></when> <when value="30203"></when> <when value="30204"></when> <when value="30205"></when> <when value="30206"></when> <when value="30207"></when> </conditional> </when> <when value="303"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="30301">Diacylglycerophosphoserines [GP0301]</option> <option value="30302">1-alkyl,2-acylglycerophosphoserines [GP0302]</option> <option value="30303">1-(1Z-alkenyl),2-acylglycerophosphoserines [GP0303]</option> <option value="30304">Dialkylglycerophosphoserines [GP0304]</option> <option value="30305">Monoacylglycerophosphoserines [GP0305]</option> <option value="30306">Monoalkylglycerophosphoserines [GP0306]</option> <option value="30307">1Z-alkenylglycerophosphoserines [GP0307]</option> <option value="NA_303" selected="True">No subclass selected</option> </param> <when value="NA_303"></when> <when value="30301"></when> <when value="30302"></when> <when value="30303"></when> <when value="30304"></when> <when value="30305"></when> <when value="30306"></when> <when value="30307"></when> </conditional> </when> <when value="304"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="30401">Diacylglycerophosphoglycerols [GP0401]</option> <option value="30402">1-alkyl,2-acylglycerophosphoglycerols [GP0402]</option> <option value="30411">1-acyl,2-alkylglycerophosphoglycerols [GP0411]</option> <option value="30403">1-(1Z-alkenyl),2-acylglycerophosphoglycerols [GP0403]</option> <option value="30404">Dialkylglycerophosphoglycerols [GP0404]</option> <option value="30405">Monoacylglycerophosphoglycerols [GP0405]</option> <option value="30406">Monoalkylglycerophosphoglycerols [GP0406]</option> <option value="30407">1Z-alkenylglycerophosphoglycerols [GP0407]</option> <option value="30408">Diacylglycerophosphodiradylglycerols [GP0408]</option> <option value="30409">Diacylglycerophosphomonoradylglycerols [GP0409]</option> <option value="30410">Monoacylglycerophosphomonoradylglycerols [GP0410]</option> <option value="NA_304" selected="True">No subclass selected</option> </param> <when value="NA_304"></when> <when value="30401"></when> <when value="30402"></when> <when value="30411"></when> <when value="30403"></when> <when value="30404"></when> <when value="30405"></when> <when value="30406"></when> <when value="30407"></when> <when value="30408"></when> <when value="30409"></when> <when value="30410"></when> </conditional> </when> <when value="305"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="30501">Diacylglycerophosphoglycerophosphates [GP0501]</option> <option value="30502">1-alkyl,2-acylglycerophosphoglycerophosphates [GP0502]</option> <option value="30503">1-(1Z-alkenyl),2-acylglycerophosphoglycerophosphates [GP0503]</option> <option value="30504">Dialkylglycerophosphoglycerophosphates [GP0504]</option> <option value="30505">Monoacylglycerophosphoglycerophosphates [GP0505]</option> <option value="30506">Monoalkylglycerophosphoglycerophosphates [GP0506]</option> <option value="30507">1Z-alkenylglycerophosphoglycerophosphates [GP0507]</option> <option value="NA_305" selected="True">No subclass selected</option> </param> <when value="NA_305"></when> <when value="30501"></when> <when value="30502"></when> <when value="30503"></when> <when value="30504"></when> <when value="30505"></when> <when value="30506"></when> <when value="30507"></when> </conditional> </when> <when value="306"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="30601">Diacylglycerophosphoinositols [GP0601]</option> <option value="30602">1-alkyl,2-acylglycerophosphoinositols [GP0602]</option> <option value="30603">1-(1Z-alkenyl),2-acylglycerophosphoinositols [GP0603]</option> <option value="30604">Dialkylglycerophosphoinositols [GP0604]</option> <option value="30605">Monoacylglycerophosphoinositols [GP0605]</option> <option value="30606">Monoalkylglycerophosphoinositols [GP0606]</option> <option value="30607">1Z-alkenylglycerophosphoinositols [GP0607]</option> <option value="NA_306" selected="True">No subclass selected</option> </param> <when value="NA_306"></when> <when value="30601"></when> <when value="30602"></when> <when value="30603"></when> <when value="30604"></when> <when value="30605"></when> <when value="30606"></when> <when value="30607"></when> </conditional> </when> <when value="307"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="30701">Diacylglycerophosphoinositol monophosphates [GP0701]</option> <option value="30702">1-alkyl,2-acylglycerophosphoinositol monophosphates [GP0702]</option> <option value="30703">1-(1Z-alkenyl),2-acylglycerophosphoinositol monophosphates [GP0703]</option> <option value="30704">Dialkylglycerophosphoinositol monophosphates [GP0704]</option> <option value="30705">Monoacylglycerophosphoinositol monophosphates [GP0705]</option> <option value="30706">Monoalkylglycerophosphoinositol monophosphates [GP0706]</option> <option value="30707">1Z-alkenylglycerophosphoinositol monophosphates [GP0707]</option> <option value="NA_307" selected="True">No subclass selected</option> </param> <when value="NA_307"></when> <when value="30701"></when> <when value="30702"></when> <when value="30703"></when> <when value="30704"></when> <when value="30705"></when> <when value="30706"></when> <when value="30707"></when> </conditional> </when> <when value="308"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="30801">Diacylglycerophosphoinositol bisphosphates [GP0801]</option> <option value="30802">1-alkyl,2-acylglycerophosphoinositol bisphosphates [GP0802]</option> <option value="30803">1-(1Z-alkenyl),2-acylglycerophosphoinositol bisphosphates [GP0803]</option> <option value="30804">Monoacylglycerophosphoinositol bisphosphates [GP0804]</option> <option value="30805">Monoalkylglycerophosphoinositol bisphosphates [GP0805]</option> <option value="30806">1Z-alkenylglycerophosphoinositol bisphosphates [GP0806]</option> <option value="NA_308" selected="True">No subclass selected</option> </param> <when value="NA_308"></when> <when value="30801"></when> <when value="30802"></when> <when value="30803"></when> <when value="30804"></when> <when value="30805"></when> <when value="30806"></when> </conditional> </when> <when value="309"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="30901">Diacylglycerophosphoinositol trisphosphates [GP0901]</option> <option value="30902">1-alkyl,2-acylglycerophosphoinositol trisphosphates [GP0902]</option> <option value="30903">1-(1Z-alkenyl),2-acylglycerophosphoinositol trisphosphates [GP0903]</option> <option value="30904">Monoacylglycerophosphoinositol trisphosphates [GP0904]</option> <option value="30905">Monoalkylglycerophosphoinositol trisphosphates [GP0905]</option> <option value="30906">1Z-alkenylglycerophosphoinositol trisphosphates [GP0906]</option> <option value="NA_309" selected="True">No subclass selected</option> </param> <when value="NA_309"></when> <when value="30901"></when> <when value="30902"></when> <when value="30903"></when> <when value="30904"></when> <when value="30905"></when> <when value="30906"></when> </conditional> </when> <when value="310"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="31001">Diacylglycerophosphates [GP1001]</option> <option value="31002">1-alkyl,2-acylglycerophosphates [GP1002]</option> <option value="31003">1-(1Z-alkenyl),2-acylglycerophosphates [GP1003]</option> <option value="31004">Dialkylglycerophosphates [GP1004]</option> <option value="31005">Monoacylglycerophosphates [GP1005]</option> <option value="31006">Monoalkylglycerophosphates [GP1006]</option> <option value="31007">1Z-alkenylglycerophosphates [GP1007]</option> <option value="NA_310" selected="True">No subclass selected</option> </param> <when value="NA_310"></when> <when value="31001"></when> <when value="31002"></when> <when value="31003"></when> <when value="31004"></when> <when value="31005"></when> <when value="31006"></when> <when value="31007"></when> </conditional> </when> <when value="311"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="31101">Diacylglyceropyrophosphates [GP1101]</option> <option value="31102">Monoacylglyceropyrophosphates [GP1102]</option> <option value="NA_311" selected="True">No subclass selected</option> </param> <when value="NA_311"></when> <when value="31101"></when> <when value="31102"></when> </conditional> </when> <when value="312"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="31201">Diacylglycerophosphoglycerophosphodiradylglycerols [GP1201]</option> <option value="31202">Diacylglycerophosphoglycerophosphomonoradylglycerols [GP1202]</option> <option value="31203">1-alkyl,2-acylglycerophosphoglycerophosphodiradylglycerols [GP1203]</option> <option value="31204">1-alkyl,2-acylglycerophosphoglycerophosphomonoradylglycerols [GP1204]</option> <option value="31205">1-(1Z-alkenyl),2-acylglycerophosphoglycerophosphodiradylglycerols [GP1205]</option> <option value="31206">1-(1Z-alkenyl),2-acylglycerophosphoglycerophosphomonoradylglycerols [GP1206]</option> <option value="31212">Dialkylglycerophosphoglycerophosphodiradylglycerols [GP1212]</option> <option value="31213">Dialkylglycerophosphoglycerophosphomonoradylglycerols [GP1213]</option> <option value="31207">Monoacylglycerophosphoglycerophosphomonoradylglycerols [GP1207]</option> <option value="31208">Monoalkylglycerophosphoglycerophosphodiradylglycerols [GP1208]</option> <option value="31209">Monoalkylglycerophosphoglycerophosphomonoradylglycerols [GP1209]</option> <option value="31210">1Z-alkenylglycerophosphoglycerophosphodiradylglycerols [GP1210]</option> <option value="31211">1Z-alkenylglycerophosphoglycerophosphomonoradylglycerols [GP1211]</option> <option value="NA_312" selected="True">No subclass selected</option> </param> <when value="NA_312"></when> <when value="31201"></when> <when value="31202"></when> <when value="31203"></when> <when value="31204"></when> <when value="31205"></when> <when value="31206"></when> <when value="31212"></when> <when value="31213"></when> <when value="31207"></when> <when value="31208"></when> <when value="31209"></when> <when value="31210"></when> <when value="31211"></when> </conditional> </when> <when value="313"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="31301">CDP-diacylglycerols [GP1301]</option> <option value="31302">CDP-1-alkyl,2-acylglycerols [GP1302]</option> <option value="31303">CDP-1-(1Z-alkenyl),2-acylglycerols [GP1303]</option> <option value="31304">CDP-Dialkylglycerols [GP1304]</option> <option value="31305">CDP-Monoacylglycerols [GP1305]</option> <option value="31306">CDP-Monoalkylglycerols [GP1306]</option> <option value="31307">CDP-1Z-alkenylglycerols [GP1307]</option> <option value="NA_313" selected="True">No subclass selected</option> </param> <when value="NA_313"></when> <when value="31301"></when> <when value="31302"></when> <when value="31303"></when> <when value="31304"></when> <when value="31305"></when> <when value="31306"></when> <when value="31307"></when> </conditional> </when> <when value="314"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="31401">Diacylglycosylglycerophospholipids [GP1401]</option> <option value="31402">1-alkyl,2-acylglycosylglycerophospholipids [GP1402]</option> <option value="31403">1-(1Z-alkenyl),2-acylglycosylglycerophospholipids [GP1403]</option> <option value="31407">Dialkylglycosylglycerophospholipids [GP1407]</option> <option value="31404">Monoacylglycosylglycerophospholipids [GP1404]</option> <option value="31405">Monoalkylglycosylglycerophospholipids [GP1405]</option> <option value="31406">1Z-alkenylglycosylglycerophospholipids [GP1406]</option> <option value="NA_314" selected="True">No subclass selected</option> </param> <when value="NA_314"></when> <when value="31401"></when> <when value="31402"></when> <when value="31403"></when> <when value="31407"></when> <when value="31404"></when> <when value="31405"></when> <when value="31406"></when> </conditional> </when> <when value="315"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="31501">Diacylglycerophosphoinositolglycans [GP1501]</option> <option value="31502">1-alkyl,2-acylglycerophosphoinositolglycans [GP1502]</option> <option value="31503">1-(1Z-alkenyl),2-acylglycerophosphoinositolglycans [GP1503]</option> <option value="31507">Dialkylglycerophosphoinositolglycans [GP1507]</option> <option value="31504">Monoacylglycerophosphoinositolglycans [GP1504]</option> <option value="31505">Monoalkylglycerophosphoinositolglycans [GP1505]</option> <option value="31506">1Z-alkenylglycerophosphoinositolglycans [GP1506]</option> <option value="NA_315" selected="True">No subclass selected</option> </param> <when value="NA_315"></when> <when value="31501"></when> <when value="31502"></when> <when value="31503"></when> <when value="31507"></when> <when value="31504"></when> <when value="31505"></when> <when value="31506"></when> </conditional> </when> <when value="316"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="31601">Diacylglycerophosphonocholines [GP1601]</option> <option value="31602">1-alkyl,2-acylglycerophosphonocholines [GP1602]</option> <option value="31603">1-(1Z-alkenyl),2-acylglycerophosphonocholines [GP1603]</option> <option value="31604">Dialkylglycerophosphonocholines [GP1604]</option> <option value="31605">Monoacylglycerophosphonocholines [GP1605]</option> <option value="31606">Monoalkylglycerophosphonocholines [GP1606]</option> <option value="31607">1Z-alkenylglycerophosphonocholines [GP1607]</option> <option value="NA_316" selected="True">No subclass selected</option> </param> <when value="NA_316"></when> <when value="31601"></when> <when value="31602"></when> <when value="31603"></when> <when value="31604"></when> <when value="31605"></when> <when value="31606"></when> <when value="31607"></when> </conditional> </when> <when value="317"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="31701">Diacylglycerophosphonoethanolamines [GP1701]</option> <option value="31702">1-alkyl,2-acylglycerophosphonoethanolamines [GP1702]</option> <option value="31703">1-(1Z-alkenyl),2-acylglycerophosphonoethanolamines [GP1703]</option> <option value="31704">Dialkylglycerophosphonoethanolamines [GP1704]</option> <option value="31705">Monoacylglycerophosphonoethanolamines [GP1705]</option> <option value="31706">Monoalkylglycerophosphonoethanolamines [GP1706]</option> <option value="31707">1Z-alkenylglycerophosphonoethanolamines [GP1707]</option> <option value="NA_317" selected="True">No subclass selected</option> </param> <when value="NA_317"></when> <when value="31701"></when> <when value="31702"></when> <when value="31703"></when> <when value="31704"></when> <when value="31705"></when> <when value="31706"></when> <when value="31707"></when> </conditional> </when> <when value="318"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_318">No subclass available</option> </param> <when value="NA_318"></when> </conditional> </when> <when value="319"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_319">No subclass available</option> </param> <when value="NA_319"></when> </conditional> </when> <when value="320"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="32001">Oxidized glycerophosphocholines [GP2001]</option> <option value="32002">Oxidized glycerophosphoethanolamines [GP2002]</option> <option value="32003">Oxidized Cardiolipins [GP2003]</option> <option value="NA_320" selected="True">No subclass selected</option> </param> <when value="NA_320"></when> <when value="32001"></when> <when value="32002"></when> <when value="32003"></when> </conditional> </when> <when value="300"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_300">No subclass available</option> </param> <when value="NA_300"></when> </conditional> </when> </conditional> </when> <when value="4"> <conditional name="select_class"> <param name="filter_class" label="Select a Lipid main class for your query " type="select"> <option value="401">Sphingoid bases [SP01]</option> <option value="402">Ceramides [SP02]</option> <option value="403">Phosphosphingolipids [SP03]</option> <option value="404">Phosphonosphingolipids [SP04]</option> <option value="405">Neutral glycosphingolipids [SP05]</option> <option value="406">Acidic glycosphingolipids [SP06]</option> <option value="407">Basic glycosphingolipids [SP07]</option> <option value="408">Amphoteric glycosphingolipids [SP08]</option> <option value="409">Arsenosphingolipids [SP09]</option> <option value="400">Other Sphingolipids [SP00]</option> <option value="NA_4" selected="True">No main class selected</option> </param> <when value="NA_4"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_400">No subclass available</option> </param> <when value="NA_400"></when> </conditional> </when> <when value="401"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="40101">Sphing-4-enines (Sphingosines) [SP0101]</option> <option value="40102">Sphinganines [SP0102]</option> <option value="40103">4-Hydroxysphinganines (Phytosphingosines) [SP0103]</option> <option value="40104">Sphingoid base homologs and variants [SP0104]</option> <option value="40105">Sphingoid base 1-phosphates [SP0105]</option> <option value="40106">Lysosphingomyelins and lysoglycosphingolipids [SP0106]</option> <option value="40107">N-methylated sphingoid bases [SP0107]</option> <option value="40108">Sphingoid base analogs [SP0108]</option> <option value="NA_401" selected="True">No subclass selected</option> </param> <when value="NA_401"></when> <when value="40101"></when> <when value="40102"></when> <when value="40103"></when> <when value="40104"></when> <when value="40105"></when> <when value="40106"></when> <when value="40107"></when> <when value="40108"></when> </conditional> </when> <when value="402"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="40201">N-acylsphingosines (ceramides) [SP0201]</option> <option value="40202">N-acylsphinganines (dihydroceramides) [SP0202]</option> <option value="40203">N-acyl-4-hydroxysphinganines (phytoceramides) [SP0203]</option> <option value="40204">Acylceramides [SP0204]</option> <option value="40205">Ceramide 1-phosphates [SP0205]</option> <option value="NA_402" selected="True">No subclass selected</option> </param> <when value="NA_402"></when> <when value="40201"></when> <when value="40202"></when> <when value="40203"></when> <when value="40204"></when> <when value="40205"></when> </conditional> </when> <when value="403"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="40301">Ceramide phosphocholines (sphingomyelins) [SP0301]</option> <option value="40302">Ceramide phosphoethanolamines [SP0302]</option> <option value="40303">Ceramide phosphoinositols [SP0303]</option> <option value="NA_403" selected="True">No subclass selected</option> </param> <when value="NA_403"></when> <when value="40301"></when> <when value="40302"></when> <when value="40303"></when> </conditional> </when> <when value="404"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_404">No subclass available</option> </param> <when value="NA_404"></when> </conditional> </when> <when value="405"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="40501">Simple Glc series [SP0501]</option> <option value="40502">GalNAcß1-3Gala1-4Galß1-4Glc- (Globo series) [SP0502]</option> <option value="40503">GalNAcß1-4Galß1-4Glc- (Ganglio series) [SP0503]</option> <option value="40504">Galß1-3GlcNAcß1-3Galß1-4Glc- (Lacto series) [SP0504]</option> <option value="40505">Galß1-4GlcNAcß1-3Galß1-4Glc- (Neolacto series) [SP0505]</option> <option value="40506">GalNAcß1-3Gala1-3Galß1-4Glc- (Isoglobo series) [SP0506]</option> <option value="40507">GlcNAcß1-2Mana1-3Manß1-4Glc- (Mollu series) [SP0507]</option> <option value="40508">GalNAcß1-4GlcNAcß1-3Manß1-4Glc- (Arthro series) [SP0508]</option> <option value="40509">Gal- (Gala series) [SP0509]</option> <option value="40500">Other Neutral glycosphingolipids [SP0500]</option> <option value="NA_405" selected="True">No subclass selected</option> </param> <when value="NA_405"></when> <when value="40501"></when> <when value="40502"></when> <when value="40503"></when> <when value="40504"></when> <when value="40505"></when> <when value="40506"></when> <when value="40507"></when> <when value="40508"></when> <when value="40509"></when> <when value="40500"></when> </conditional> </when> <when value="406"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="40601">Gangliosides [SP0601]</option> <option value="40602">Sulfoglycosphingolipids (sulfatides) [SP0602]</option> <option value="40603">Glucuronosphingolipids [SP0603]</option> <option value="40604">Phosphoglycosphingolipids [SP0604]</option> <option value="40600">Other Acidic glycosphingolipids [SP0600]</option> <option value="NA_406" selected="True">No subclass selected</option> </param> <when value="NA_406"></when> <when value="40601"></when> <when value="40602"></when> <when value="40603"></when> <when value="40604"></when> <when value="40600"></when> </conditional> </when> <when value="407"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_407">No subclass available</option> </param> <when value="NA_407"></when> </conditional> </when> <when value="408"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_408">No subclass available</option> </param> <when value="NA_408"></when> </conditional> </when> <when value="409"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_409">No subclass available</option> </param> <when value="NA_409"></when> </conditional> </when> <when value="400"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_400">No subclass available</option> </param> <when value="NA_400"></when> </conditional> </when> </conditional> </when> <when value="5"> <conditional name="select_class"> <param name="filter_class" label="Select a Lipid main class for your query " type="select"> <option value="501">Sterols [ST01]</option> <option value="502">Steroids [ST02]</option> <option value="503">Secosteroids [ST03]</option> <option value="504">Bile acids and derivatives [ST04]</option> <option value="505">Steroid conjugates [ST05]</option> <option value="500">Other Sterol lipids [ST00]</option> <option value="NA_5" selected="True">No main class selected</option> </param> <when value="NA_5"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_500">No subclass available</option> </param> <when value="NA_500"></when> </conditional> </when> <when value="501"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="50101">Cholesterol and derivatives [ST0101]</option> <option value="50102">Steryl esters [ST0102]</option> <option value="50103">Ergosterols and C24-methyl derivatives [ST0103]</option> <option value="50104">Stigmasterols and C24-ethyl derivatives [ST0104]</option> <option value="50105">C24-propyl sterols and derivatives [ST0105]</option> <option value="50106">Gorgosterols and derivatives [ST0106]</option> <option value="50107">Furostanols and derivatives [ST0107]</option> <option value="50108">Spirostanols and derivatives [ST0108]</option> <option value="50109">Furospirostanols and derivatives [ST0109]</option> <option value="50110">Cycloartanols and derivatives [ST0110]</option> <option value="50111">Calysterols and cyclopropyl sidechain derivatives [ST0111]</option> <option value="50112">Cardanolides and derivatives [ST0112]</option> <option value="50113">Bufanolides and derivatives [ST0113]</option> <option value="50114">Brassinolides and derivatives [ST0114]</option> <option value="50115">Solanidines and alkaloid derivatives [ST0115]</option> <option value="50116">Withanolides and derivatives [ST0116]</option> <option value="NA_501" selected="True">No subclass selected</option> </param> <when value="NA_501"></when> <when value="50101"></when> <when value="50102"></when> <when value="50103"></when> <when value="50104"></when> <when value="50105"></when> <when value="50106"></when> <when value="50107"></when> <when value="50108"></when> <when value="50109"></when> <when value="50110"></when> <when value="50111"></when> <when value="50112"></when> <when value="50113"></when> <when value="50114"></when> <when value="50115"></when> <when value="50116"></when> </conditional> </when> <when value="502"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="50201">C18 steroids (estrogens) and derivatives [ST0201]</option> <option value="50202">C19 steroids (androgens) and derivatives [ST0202]</option> <option value="50203">C21 steroids (gluco/mineralocorticoids, progestogins) and derivatives [ST0203]</option> <option value="NA_502" selected="True">No subclass selected</option> </param> <when value="NA_502"></when> <when value="50201"></when> <when value="50202"></when> <when value="50203"></when> </conditional> </when> <when value="503"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="50301">Vitamin D2 and derivatives [ST0301]</option> <option value="50302">Vitamin D3 and derivatives [ST0302]</option> <option value="50303">Vitamin D4 and derivatives [ST0303]</option> <option value="50304">Vitamin D5 and derivatives [ST0304]</option> <option value="50305">Vitamin D6 and derivatives [ST0305]</option> <option value="50306">Vitamin D7 and derivatives [ST0306]</option> <option value="NA_503" selected="True">No subclass selected</option> </param> <when value="NA_503"></when> <when value="50301"></when> <when value="50302"></when> <when value="50303"></when> <when value="50304"></when> <when value="50305"></when> <when value="50306"></when> </conditional> </when> <when value="504"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="50401">C24 bile acids, alcohols, and derivatives [ST0401]</option> <option value="50402">C26 bile acids, alcohols, and derivatives [ST0402]</option> <option value="50403">C27 bile acids, alcohols, and derivatives [ST0403]</option> <option value="50404">C28 bile acids, alcohols, and derivatives [ST0404]</option> <option value="50405">C22 bile acids, alcohols, and derivatives [ST0405]</option> <option value="50406">C23 bile acids, alcohols, and derivatives [ST0406]</option> <option value="50407">C25 bile acids, alcohols, and derivatives [ST0407]</option> <option value="50408">C29 bile acids, alcohols, and derivatives [ST0408]</option> <option value="NA_504" selected="True">No subclass selected</option> </param> <when value="NA_504"></when> <when value="50401"></when> <when value="50402"></when> <when value="50403"></when> <when value="50404"></when> <when value="50405"></when> <when value="50406"></when> <when value="50407"></when> <when value="50408"></when> </conditional> </when> <when value="505"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="50501">Glucuronides [ST0501]</option> <option value="50502">Sulfates [ST0502]</option> <option value="50503">Glycine conjugates [ST0503]</option> <option value="50504">Taurine conjugates [ST0504]</option> <option value="50505">Other Steroid conjugates [ST0505]</option> <option value="NA_505" selected="True">No subclass selected</option> </param> <when value="NA_505"></when> <when value="50501"></when> <when value="50502"></when> <when value="50503"></when> <when value="50504"></when> <when value="50505"></when> </conditional> </when> <when value="500"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_500">No subclass available</option> </param> <when value="NA_500"></when> </conditional> </when> </conditional> </when> <when value="6"> <conditional name="select_class"> <param name="filter_class" label="Select a Lipid main class for your query " type="select"> <option value="601">Isoprenoids [PR01]</option> <option value="602">Quinones and hydroquinones [PR02]</option> <option value="603">Polyprenols [PR03]</option> <option value="604">Hopanoids [PR04]</option> <option value="600">Other Prenol lipids [PR00]</option> <option value="NA_6" selected="True">No main class selected</option> </param> <when value="NA_6"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_600">No subclass available</option> </param> <when value="NA_600"></when> </conditional> </when> <when value="601"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="60101">C5 isoprenoids (hemiterpenes) [PR0101]</option> <option value="60102">C10 isoprenoids (monoterpenes) [PR0102]</option> <option value="60103">C15 isoprenoids (sesquiterpenes) [PR0103]</option> <option value="60104">C20 isoprenoids (diterpenes) [PR0104]</option> <option value="60105">C25 isoprenoids (sesterterpenes) [PR0105]</option> <option value="60106">C30 isoprenoids (triterpenes) [PR0106]</option> <option value="60107">C40 isoprenoids (tetraterpenes) [PR0107]</option> <option value="60108">Polyterpenes [PR0108]</option> <option value="60109">Retinoids [PR0109]</option> <option value="NA_601" selected="True">No subclass selected</option> </param> <when value="NA_601"></when> <when value="60101"></when> <when value="60102"></when> <when value="60103"></when> <when value="60104"></when> <when value="60105"></when> <when value="60106"></when> <when value="60107"></when> <when value="60108"></when> <when value="60109"></when> </conditional> </when> <when value="602"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="60201">Ubiquinones [PR0201]</option> <option value="60202">Vitamin E [PR0202]</option> <option value="60203">Vitamin K [PR0203]</option> <option value="NA_602" selected="True">No subclass selected</option> </param> <when value="NA_602"></when> <when value="60201"></when> <when value="60202"></when> <when value="60203"></when> </conditional> </when> <when value="603"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="60301">Bactoprenols [PR0301]</option> <option value="60302">Bactoprenol monophosphates [PR0302]</option> <option value="60303">Bactoprenol diphosphates [PR0303]</option> <option value="60304">Phytoprenols [PR0304]</option> <option value="60305">Phytoprenol monophosphates [PR0305]</option> <option value="60306">Phytoprenol diphosphates [PR0306]</option> <option value="60307">Dolichols [PR0307]</option> <option value="60308">Dolichol monophosphates [PR0308]</option> <option value="60309">Dolichol diphosphates [PR0309]</option> <option value="NA_603" selected="True">No subclass selected</option> </param> <when value="NA_603"></when> <when value="60301"></when> <when value="60302"></when> <when value="60303"></when> <when value="60304"></when> <when value="60305"></when> <when value="60306"></when> <when value="60307"></when> <when value="60308"></when> <when value="60309"></when> </conditional> </when> <when value="604"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_604">No subclass available</option> </param> <when value="NA_604"></when> </conditional> </when> <when value="600"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_600">No subclass available</option> </param> <when value="NA_600"></when> </conditional> </when> </conditional> </when> <when value="7"> <conditional name="select_class"> <param name="filter_class" label="Select a Lipid main class for your query " type="select"> <option value="701">Acylaminosugars [SL01]</option> <option value="702">Acylaminosugar glycans [SL02]</option> <option value="703">Acyltrehaloses [SL03]</option> <option value="704">Acyltrehalose glycans [SL04]</option> <option value="705">Other acyl sugars [SL05]</option> <option value="700">Other Saccharolipids [SL00]</option> <option value="NA_7" selected="True">No main class selected</option> </param> <when value="NA_7"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_700">No subclass available</option> </param> <when value="NA_700"></when> </conditional> </when> <when value="701"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="70101">Monoacylaminosugars [SL0101]</option> <option value="70102">Diacylaminosugars [SL0102]</option> <option value="70103">Triacylaminosugars [SL0103]</option> <option value="70104">Tetraacylaminosugars [SL0104]</option> <option value="70105">Pentaacylaminosugars [SL0105]</option> <option value="70106">Hexaacylaminosugars [SL0106]</option> <option value="70107">Heptaacylaminosugars [SL0107]</option> <option value="NA_701" selected="True">No subclass selected</option> </param> <when value="NA_701"></when> <when value="70101"></when> <when value="70102"></when> <when value="70103"></when> <when value="70104"></when> <when value="70105"></when> <when value="70106"></when> <when value="70107"></when> </conditional> </when> <when value="702"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_702">No subclass available</option> </param> <when value="NA_702"></when> </conditional> </when> <when value="703"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_703">No subclass available</option> </param> <when value="NA_703"></when> </conditional> </when> <when value="704"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_704">No subclass available</option> </param> <when value="NA_704"></when> </conditional> </when> <when value="705"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_705">No subclass available</option> </param> <when value="NA_705"></when> </conditional> </when> <when value="700"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_700">No subclass available</option> </param> <when value="NA_700"></when> </conditional> </when> </conditional> </when> <when value="8"> <conditional name="select_class"> <param name="filter_class" label="Select a Lipid main class for your query " type="select"> <option value="801">Linear polyketides [PK01]</option> <option value="802">Halogenated acetogenins [PK02]</option> <option value="803">Annonaceae acetogenins [PK03]</option> <option value="804">Macrolides and lactone polyketides [PK04]</option> <option value="805">Ansamycins and related polyketides [PK05]</option> <option value="806">Polyenes [PK06]</option> <option value="807">Linear tetracyclines [PK07]</option> <option value="808">Angucyclines [PK08]</option> <option value="809">Polyether polyketides [PK09]</option> <option value="810">Aflatoxins and related substances [PK10]</option> <option value="811">Cytochalasins [PK11]</option> <option value="812">Flavonoids [PK12]</option> <option value="813">Aromatic polyketides [PK13]</option> <option value="814">Non-ribosomal peptide/polyketide hybrids [PK14]</option> <option value="800">Other Polyketides [PK00]</option> <option value="NA_8" selected="True">No main class selected</option> </param> <when value="NA_8"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_800">No subclass available</option> </param> <when value="NA_800"></when> </conditional> </when> <when value="801"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_801">No subclass available</option> </param> <when value="NA_801"></when> </conditional> </when> <when value="802"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_802">No subclass available</option> </param> <when value="NA_802"></when> </conditional> </when> <when value="803"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_803">No subclass available</option> </param> <when value="NA_803"></when> </conditional> </when> <when value="804"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_804">No subclass available</option> </param> <when value="NA_804"></when> </conditional> </when> <when value="805"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_805">No subclass available</option> </param> <when value="NA_805"></when> </conditional> </when> <when value="806"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_806">No subclass available</option> </param> <when value="NA_806"></when> </conditional> </when> <when value="807"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_807">No subclass available</option> </param> <when value="NA_807"></when> </conditional> </when> <when value="808"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_808">No subclass available</option> </param> <when value="NA_808"></when> </conditional> </when> <when value="809"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_809">No subclass available</option> </param> <when value="NA_809"></when> </conditional> </when> <when value="810"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_810">No subclass available</option> </param> <when value="NA_810"></when> </conditional> </when> <when value="811"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_811">No subclass available</option> </param> <when value="NA_811"></when> </conditional> </when> <when value="812"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="81201">Anthocyanidins [PK1201]</option> <option value="81202">Flavans, Flavanols and Leucoanthocyanidins [PK1202]</option> <option value="81203">Proanthocyanidins [PK1203]</option> <option value="81204">Biflavonoids and polyflavonoids [PK1204]</option> <option value="81205">Isoflavonoids [PK1205]</option> <option value="81206">Rotenoid flavonoids [PK1206]</option> <option value="81207">Pterocarpans [PK1207]</option> <option value="81208">Isoflavans [PK1208]</option> <option value="81209">Coumestan flavonoids [PK1209]</option> <option value="81210">Neoflavonoids [PK1210]</option> <option value="81211">Flavones and Flavonols [PK1211]</option> <option value="81212">Chalcones and dihydrochalcones [PK1212]</option> <option value="81213">Aurone flavonoids [PK1213]</option> <option value="81214">Flavanones [PK1214]</option> <option value="81215">Dihydroflavonols [PK1215]</option> <option value="81216">Other Flavonoids [PK1216]</option> <option value="NA_812" selected="True">No subclass selected</option> </param> <when value="NA_812"></when> <when value="81201"></when> <when value="81202"></when> <when value="81203"></when> <when value="81204"></when> <when value="81205"></when> <when value="81206"></when> <when value="81207"></when> <when value="81208"></when> <when value="81209"></when> <when value="81210"></when> <when value="81211"></when> <when value="81212"></when> <when value="81213"></when> <when value="81214"></when> <when value="81215"></when> <when value="81216"></when> </conditional> </when> <when value="813"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="81301">Monocyclic aromatic polyketides [PK1301]</option> <option value="81302">Naphthalenes and naphthoquinones [PK1302]</option> <option value="81303">Benzoisochromanquinones [PK1303]</option> <option value="81304">Anthracenes and phenanthrenes [PK1304]</option> <option value="81305">Anthracyclinones [PK1305]</option> <option value="81306">Dibenzofurans, griseofulvins, dibenzopyrans and xanthones [PK1306]</option> <option value="81307">Diphenylmethanes, acylphloroglucinols and benzophenones [PK1307]</option> <option value="81308">Depsides and depsidones [PK1308]</option> <option value="81309">Diphenyl ethers, biphenyls, dibenzyls and stilbenes [PK1309]</option> <option value="81310">Benzofuranoids [PK1310]</option> <option value="81311">Benzopyranoids [PK1311]</option> <option value="81312">Other aromatic polyketides [PK1312]</option> <option value="NA_813" selected="True">No subclass selected</option> </param> <when value="NA_813"></when> <when value="81301"></when> <when value="81302"></when> <when value="81303"></when> <when value="81304"></when> <when value="81305"></when> <when value="81306"></when> <when value="81307"></when> <when value="81308"></when> <when value="81309"></when> <when value="81310"></when> <when value="81311"></when> <when value="81312"></when> </conditional> </when> <when value="814"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_814">No subclass available</option> </param> <when value="NA_814"></when> </conditional> </when> <when value="800"> <conditional name="select_subclass"> <param name="filter_subclass" label="Select a Lipid subclass for your query " type="select"> <option value="NA_800">No subclass available</option> </param> <when value="NA_800"></when> </conditional> </when> </conditional> </when> </conditional> <!-- Part to update with new LIPIDMAPS Tax --> </when> </conditional> <param name="decimal" label="Number of significant decimal " type="select" help="Number of significant decimal of your mz."> <option value="0">0</option> <option value="1">1</option> <option value="2" selected="True">2</option> <option value="3">3</option> <option value="4">4</option> <option value="5">5</option> <option value="6">6</option> <option value="7">7</option> <option value="8">8</option> </param> <param name="round_type" label="Type of cut of the masses " type="select" display="radio" help="Example 801.1789 is truncate as 801.17 or arround as 801.18 with 2 significant decimal."> <option value="round">round</option> <option value="truncation">truncation</option> </param> <param name="tolerance" label="Mass-to-charge ratio " type="float" min="0" max="100" value="0.5" size="10" help="Default value is 0.5 for LM (mass-to-charge ratio)" /> </inputs> <outputs> <data name="variableMetadata_out" format="tabular" label="${file_input.name[:-6]}.LMSD.tabular"/> <data name="LMSDOutWeb" format="html" label="${file_input.name[:-6]}.LMSD_WEB.html"/> <data name="LMSDOutSum" format="tabular" label="${file_input.name[:-6]}.LMSD_SUM.tabular"/> </outputs> <tests> <test> <!--test 01 some results - input01_50_without_class.csv --> <param name="file_input" value="input01_50_without_class.csv"/> <param name="mode" value="NEU"/> <param name="lineheader" value="1"/> <param name="col_mass" value="3"/> <param name="tolerance" value="0.5"/> <param name="decimal" value="2"/> <param name="round_type" value="round"/> <param name="complex_query_action" value="no"/> <param name="filter_cat" value="3"/> <param name="filter_class" value="306"/> <param name="filter_subclass" value="NA_306"/> <output name="variableMetadata_out" file="out_test01.tabular"/> <output name="LMSDOutWeb" file="out_test01.html"/> <output name="LMSDOutSum" file="out_sum_test01.tabular"/> </test> <test> <!--test 02 : some results - input02_480_several_class.csv file--> <param name="file_input" value="input02_480_several_class.csv"/> <param name="mode" value="NEU"/> <param name="lineheader" value="1"/> <param name="col_mass" value="1"/> <param name="tolerance" value="0.5"/> <param name="decimal" value="2"/> <param name="round_type" value="round"/> <param name="complex_query_action" value="yes"/> <param name="col_classif_id" value="3"/> <output name="variableMetadata_out" file="out_test02.tabular"/> <output name="LMSDOutWeb" file="out_test02.html"/> <output name="LMSDOutSum" file="out_sum_test02.tabular"/> </test> <test> <!--test 03 : some results - input03_200_without_class_on_maincl_301.csv file--> <param name="file_input" value="input03_200_without_class_on_maincl_301.csv"/> <param name="mode" value="NEU"/> <param name="lineheader" value="1"/> <param name="col_mass" value="1"/> <param name="complex_query_action" value="no"/> <param name="filter_cat" value="3"/> <param name="filter_class" value="301"/> <param name="filter_subclass" value="NA_301"/> <param name="tolerance" value="0.5"/> <param name="decimal" value="2"/> <param name="round_type" value="round"/> <output name="variableMetadata_out" file="out_test03.tabular"/> <output name="LMSDOutWeb" file="out_test03.html"/> <output name="LMSDOutSum" file="out_sum_test03.tabular"/> </test> <test> <!--test 04 some results and mz transfo with the mode - input01_50_without_class.csv --> <param name="file_input" value="input01_50_without_class.csv"/> <param name="mode" value="POS"/> <param name="lineheader" value="1"/> <param name="col_mass" value="3"/> <param name="tolerance" value="0.5"/> <param name="decimal" value="2"/> <param name="round_type" value="round"/> <param name="complex_query_action" value="no"/> <param name="filter_cat" value="3"/> <param name="filter_class" value="306"/> <param name="filter_subclass" value="NA_306"/> <output name="variableMetadata_out" file="out_test04.tabular"/> <output name="LMSDOutWeb" file="out_test04.html"/> <output name="LMSDOutSum" file="out_sum_test04.tabular"/> </test> </tests> <help><![CDATA[ .. class:: infomark **Authors** Franck Giacomoni --------------------------------------------------- .. class:: infomark **Please cite** If you use this tool, please cite | `Sud M., Fahy E., Cotter D., Brown A., Dennis E., Glass C., Murphy R., Raetz C., Russell D., and Subramaniam S. LMSD: LIPID MAPS structure database. Nucleic Acids Research 35, D527-32 (2006). <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669719>`_ --------------------------------------------------- ============== LIPIDMAPS_WS ============== ----------- Description ----------- | This tool accesses to Structure Database (LMSD) by the LMSDRecord.php service. | It supports retrieval of detailed information for a specific lipid with a valid LMID. | Searches on LMSD using a variety of parameters specified below. | | LMSD querying is very long because LMSD do not allow to hit its server more often than once per 20 seconds. LMSD may have to kill scripts that hit its server more frequently. ----------------- Workflow position ----------------- .. image:: ./static/images/metabolomics/lipidmaps.png :width: 800 ----------- Input files ----------- +-------------------------+-----------+ | Parameter : num + label | Format | +=========================+===========+ | 1 : variableMetadata | tabular | +-------------------------+-----------+ Constraints file : * a column with mz * a column with containing category or class or sub class identifiants. [optionnal] ---------- Parameters ---------- Masses Column | mz list using in searches. | Each mz will be arround or truncate and querying to LMSD. Mode | Ionisation mode of the instrument (Positive/Negative or neutral) | Selecting POS or NEG will transform the given mz list into a neutral mz list permitting the use of LMSD with the right format. Actually, LMSD take neutral masses as query. | Be aware to use this option. The transformation is really pertinent for only masses corresponding to [M+H]+ or [M-H]- species | Example of transformation: initial mz from positive mode is 101.008374 and will become 100,000000 (init mass - proton mass + electron mass) if POS option is selected. Modify input masses | Select posibility to apply oxidation(s) and/or neutral loss(es) | Example : if you apply a oxidation (+ O) on a mz = 800.00, the mass search on LMSD will be 800.00 - 15.99. | A LM return will be : LMGP01010622 PC(16:0/20:3(5Z,8Z,11Z)) C44H82NO8P 783.58 but do not forget to add a Oxigen... Transform masses extracted from file with oxidation(s) | Choose : + O, + 2 O, + 4 O. Correct masses extracted from file with neutral loss : | Choose : H2O2 loss, H2O loss Perform a multiple queries on input masses | Select \'no\' to use the following classification on all mz | or \'yes\' to search each mz on one given cat/class/subclass in file column. Lipid category | Select a category in the given list Lipid main class | Select a main class in the given list Lipid subclass | Select a sub class in the given list Number of significant decimal | Number of significant decimal of your mz. This parameter will influence the arround on oxidation or neutral loss Type of cut | truncate or arround the mz with the given significant decimal number | example 801.1789 is truncate as 801.17 or arround as 801.18 with 2 significant decimal. Delta of mass | Exact mass off set (great as +/- 0.01 to +/- 100) ------------ Output files ------------ Two types of files | LMSD_WEB.html: for viewing result via HTML. | LMSD.tabular: for linking with others modules. | LMSD_SUM.tabular: for summary result by cluster - NEW. --------------- 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 | Les banques d'annotation - 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/gkl838</citation> </citations> </tool>