hmdb_ms_search: wsdl_hmdb.xml annotate

annotate wsdl_hmdb.xml @ 28:6d796927335d draft

master branch Updating with tag :CI_COMMIT_TAG - - Fxx

author	fgiacomoni
date	Tue, 04 Jun 2024 08:54:22 +0000
parents	144e4a8ad000
children	29195cb5d378

rev	line source
28 6d796927335d master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 27 diff changeset	1 <tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.5">
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	2 <description>
24 d8e2ede293a6 Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 23 diff changeset	3 search by masses on HMDB v5 online LCMS bank
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	4 </description>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	5
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	6 <requirements>
12 2203cb539e53 Master branch Updating - - Fxx fgiacomoni parents: 11 diff changeset	7 <requirement type="package" version="2.161">perl-data-dumper</requirement>
10 4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	8 <requirement type="package" version="2.97">perl-html-template</requirement>
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	9 <requirement type="package" version="1.19">perl-soap-lite</requirement>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	10 <requirement type="package" version="6.15">perl-lwp-simple</requirement>
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	11 <requirement type="package" version="6.15">perl-libwww-perl</requirement>
28 6d796927335d master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 27 diff changeset	12 <requirement type="package" version="5.17">perl-uri</requirement>
27 144e4a8ad000 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 26 diff changeset	13 <requirement type="package" version="1.1.1">perl-uri-encode</requirement>
9 c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 7 diff changeset	14 <requirement type="package" version="1.97">perl-text-csv</requirement>
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 7 diff changeset	15 <requirement type="package" version="3.52">perl-xml-twig</requirement>
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	16 <requirement type="package" version="1.91">perl-www-mechanize</requirement>
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	17 </requirements>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	18
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	19 <stdio>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	20 <exit_code range="1" level="fatal" />
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	21 </stdio>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	22
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	23
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	24 <command><![CDATA[
13 3587cb923890 Master branch Updating - - Fxx fgiacomoni parents: 12 diff changeset	25 perl $__tool_directory__/wsdl_hmdb.pl
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	26 #if str($input_type.choice) == "YES":
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	27 -masses "${input_type.masses}"
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	28 -header_choice "${input_type.header.header_choice}"
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	29 #if str($input_type.header.header_choice) == "yes":
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	30 -nblineheader "${$input_type.header.nbHeader}"
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	31 #end if
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	32 -colfactor "${input_type.colfactor}"
24 d8e2ede293a6 Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 23 diff changeset	33 -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xlsx "$HmdbOutXlsx"
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	34 #else:
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	35 -mass "${input_type.mass}"
24 d8e2ede293a6 Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 23 diff changeset	36 -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xlsx "$HmdbOutXlsx2"
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	37 #end if
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	38
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	39 -mode "${mode_type.mode}"
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	40
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	41 #if str($mode_type.mode) == "positive":
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	42 -adduct_type "${mode_type.data_positive_adducts}"
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	43 #elif str($mode_type.mode) == "negative":
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	44 -adduct_type "${mode_type.data_negative_adducts}"
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	45 #elif str($mode_type.mode) == "neutral":
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	46 -adduct_type "${mode_type.data_neutral_adducts}"
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	47 #end if
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	48
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	49 -delta "$delta" -maxquery "$maxquery"
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	50 -advancedFeatures "$advancedFeatures"
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	51 -verbose "$verbose"
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	52
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	53 ]]></command>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	54 <inputs>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	55 <conditional name="input_type">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	56 <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">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	57 <option value="YES">YES</option>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	58 <option value="NO">NO</option>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	59 </param>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	60 <when value="YES">
5 520778e357cc planemo upload commit c49b69597de7f1ce2034815e968fbf5d7c0373c4 fgiacomoni parents: 3 diff changeset	61 <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" />
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	62 <conditional name="header">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	63 <param name="header_choice" type="select" label="Do you have a header " help="if 'YES' is selected then enter your number of header lines">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	64 <option value="no">NO</option>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	65 <option value="yes" selected="true">YES</option>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	66 </param>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	67 <when value="yes">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	68 <param name="nbHeader" label="Number of header lines " type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	69 </when>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	70 <when value="no"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	71 </conditional>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	72 <param name="colfactor" label="Column of masses " type="data_column" data_ref="masses" accept_default="true" />
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	73 </when>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	74 <when value="NO">
7 ecf8e43aceda planemo upload commit d1a5cd8f1baf00879ffa44649883f91c64f43392 fgiacomoni parents: 5 diff changeset	75 <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" />
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	76 </when>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	77 </conditional>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	78
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	79 <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)"/>
21 63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	80 <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"/>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	81
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	82 <conditional name="mode_type">
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	83 <param name="mode" label="Molecular Species " type="select" display="radio" help="">
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	84 <option value="positive">Positif Mode</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	85 <option value="negative">Negatif Mode</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	86 <option value="neutral" selected="True">Neutral Mass</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	87 </param>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	88 <when value="positive">
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	89 <param name="data_positive_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	90 <option value="Unknown">Unknown</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	91 <option value="M+H" selected="True">M+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	92 <option value="M+H-2H2O">M+H-2H2O</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	93 <option value="M+H-H2O">M+H-H2O</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	94 <option value="M+NH4-H2O">M+NH4-H2O</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	95 <option value="M+Li">M+Li</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	96 <option value="M+NH4">M+NH4</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	97 <option value="M+Na">M+Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	98 <option value="M+CH3OH+H">M+CH3OH+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	99 <option value="M+K">M+K</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	100 <option value="M+ACN+H">M+ACN+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	101 <option value="M+2Na-H">M+2Na-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	102 <option value="M+IsoProp+H">M+IsoProp+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	103 <option value="M+ACN+Na">M+ACN+Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	104 <option value="M+2K-H">M+2K-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	105 <option value="M+DMSO+H">M+DMSO+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	106 <option value="M+2ACN+H">M+2ACN+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	107 <option value="M+IsoProp+Na+H">M+IsoProp+Na+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	108 <option value="M+H+HCOONa">M+H+HCOONa</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	109 <option value="2M+H">2M+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	110 <option value="2M+NH4">2M+NH4</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	111 <option value="2M+Na">2M+Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	112 <option value="2M+2H+3H2O">2M+2H+3H2O</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	113 <option value="2M+K">2M+K</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	114 <option value="2M+ACN+H">2M+ACN+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	115 <option value="2M+ACN+Na">2M+ACN+Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	116 <option value="2M+H-H2O">2M+H-H2O</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	117 <option value="M+2H">M+2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	118 <option value="M+H+NH4">M+H+NH4</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	119 <option value="M+H+Na">M+H+Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	120 <option value="M+H+K">M+H+K</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	121 <option value="M+ACN+2H">M+ACN+2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	122 <option value="M+2Na">M+2Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	123 <option value="M+2ACN+2H">M+2ACN+2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	124 <option value="M+3ACN+2H">M+3ACN+2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	125 <option value="M+3H">M+3H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	126 <option value="M+2H+Na">M+2H+Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	127 <option value="M+H+2Na">M+H+2Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	128 <option value="M+3Na">M+3Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	129 <option value="M+H+2K">M+H+2K</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	130 </param>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	131 </when>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	132 <when value="negative">
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	133 <param name="data_negative_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	134 <option value="Unknown">Unknown</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	135 <option value="M-H" selected="True">M-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	136 <option value="M-H20-H">M-H20-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	137 <option value="M+F">M+F</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	138 <option value="M+Na-2H">M+Na-2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	139 <option value="M+Cl">M+Cl</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	140 <option value="M+K-2H">M+K-2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	141 <option value="M+FA-H">M+FA-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	142 <option value="M+Hac-H">M+Hac-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	143 <option value="M+Br">M+Br</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	144 <option value="M+TFA-H">M+TFA-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	145 <option value="M-H+HCOONa">M-H+HCOONa</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	146 <option value="2M-H">2M-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	147 <option value="2M+FA-H">2M+FA-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	148 <option value="2M+Hac-H">2M+Hac-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	149 <option value="3M-H">3M-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	150 <option value="M-2H">M-2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	151 <option value="M-3H">M-3H</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	152 </param>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	153 </when>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	154 <when value="neutral">
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	155 <param name="data_neutral_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	156 <option value="Unknown">Unknown</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	157 <option value="M" selected="True">M</option>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	158 </param>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	159 </when>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	160 </conditional>
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	161
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	162
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	163
63ba1cb240b7 Prod branch Updating - - Fxx fgiacomoni parents: 18 diff changeset	164
15 beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	165 <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">
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	166 <option value="1">Advanced mode</option>
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	167 <option value="0" selected="True">Default mode</option>
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	168 </param>
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	169 <param name="verbose" type="select" label="Verbose level" display="radio" help="">
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	170 <option value="1" selected="true">Low</option>
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	171 <option value="3" >High</option>
beb9619263b0 Master branch Updating - - Fxx fgiacomoni parents: 14 diff changeset	172 </param>
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	173 </inputs>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	174
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	175 <outputs>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	176 <data name="variableMetadata" format="tabular" label="${input_type.masses.name[:-6]}.HMDB.tabular">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	177 <filter>input_type['choice'] == "YES"</filter>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	178 </data>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	179 <data name="HmdbOutWeb" format="html" label="${input_type.masses.name[:-6]}.HMDB_WEB.html">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	180 <filter>input_type['choice'] == "YES"</filter>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	181 </data>
2 a3744fb3605c planemo upload commit e3e676478019ab709f0043c09b02ba93e042957f fgiacomoni parents: 1 diff changeset	182 <data name="HmdbOutXlsx" label="${input_type.masses.name[:-6]}.HMDB_XLS.txt" format="tabular">
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	183 <filter>input_type['choice'] == "YES"</filter>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	184 </data>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	185 <data name="variableMetadata2" format="tabular" label="HMDB.tabular">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	186 <filter>input_type['choice'] == "NO"</filter>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	187 </data>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	188 <data name="HmdbOutWeb2" format="html" label="HMDB_WEB.html">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	189 <filter>input_type['choice'] == "NO"</filter>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	190 </data>
2 a3744fb3605c planemo upload commit e3e676478019ab709f0043c09b02ba93e042957f fgiacomoni parents: 1 diff changeset	191 <data name="HmdbOutXlsx2" label="HMDB_XLS.txt" format="tabular">
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	192 <filter>input_type['choice'] == "NO"</filter>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	193 </data>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	194 </outputs>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	195
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	196 <tests>
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 13 diff changeset	197 <!--test 01 no result - fake-mzrt-input-with-id -->
625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 13 diff changeset	198 <!--
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	199 <test>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	200 <param name="choice" value="YES"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	201 <param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	202 <param name="header_choice" value="yes"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	203 <param name="nblineheader" value="1"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	204 <param name="colfactor" value="2"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	205 <param name="delta" value="0.001"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	206 <param name="mode" value="neutral"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	207 <param name="maxquery" value="5"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	208 <output name="variableMetadata" file="out_test01.tabular"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	209 <output name="HmdbOutWeb" file="out_test01.html"/>
2 a3744fb3605c planemo upload commit e3e676478019ab709f0043c09b02ba93e042957f fgiacomoni parents: 1 diff changeset	210 <output name="HmdbOutXlsx" file="out_test01.txt"/>
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	211 </test>
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 13 diff changeset	212 -->
625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 13 diff changeset	213 <!--test 02 : some results - with-mzrt-input-with-id file-->
625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 13 diff changeset	214 <!--
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	215 <test>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	216 <param name="choice" value="YES"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	217 <param name="masses" value="input_test02_mzrt-input-with-id.tabular"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	218 <param name="header_choice" value="yes"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	219 <param name="nblineheader" value="1"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	220 <param name="colfactor" value="2"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	221 <param name="delta" value="0.001"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	222 <param name="mode" value="positive"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	223 <param name="maxquery" value="5"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	224 <output name="variableMetadata" file="out_test02.tabular"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	225 <output name="HmdbOutWeb" file="out_test02.html"/>
2 a3744fb3605c planemo upload commit e3e676478019ab709f0043c09b02ba93e042957f fgiacomoni parents: 1 diff changeset	226 <output name="HmdbOutXlsx" file="out_test02.txt"/>
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	227 </test>
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 13 diff changeset	228 -->
625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 13 diff changeset	229 <!--test 03 : some results - with-mz list in manual mass mode-->
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	230 <test>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	231 <param name="choice" value="NO"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	232 <param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	233 <param name="delta" value="0.05"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	234 <param name="mode" value="positive"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	235 <param name="maxquery" value="5"/>
26 76872ac24fb2 master branch Updating with tag :CI_COMMIT_TAG - - Fxx fgiacomoni parents: 25 diff changeset	236 <param name="data_positive_adducts" value="M+H"/>
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	237 <output name="variableMetadata2" file="out_test03.tabular"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	238 <output name="HmdbOutWeb2" file="out_test03.html"/>
2 a3744fb3605c planemo upload commit e3e676478019ab709f0043c09b02ba93e042957f fgiacomoni parents: 1 diff changeset	239 <output name="HmdbOutXlsx2" file="out_test03.txt"/>
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	240 </test>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	241 </tests>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	242
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	243 <help><![CDATA[
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	244
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	245 .. class:: infomark
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	246
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	247 Authors Marion Landi, Yann Guitton and Franck Giacomoni
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	248
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	249 ---------------------------------------------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	250
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	251 .. class:: infomark
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	252
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	253 Please cite If you use this tool, please add the following reference
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	254 \| 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.
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 13 diff changeset	255 \| 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.
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	256 \| Wishart DS et al, HMDB 5.0 - the Human Metabolome Database for 2022, Nucleic Acids Res. 2022.
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	257
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	258
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	259 ---------------------------------------------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	260
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	261 ==============
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	262 HMDB MS search
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	263 ==============
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	264
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	265 -----------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	266 Description
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	267 -----------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	268
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	269 \| Search informations (like : HMDB id, Name, Adduct, delta mass) on HMDB online bank
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	270 \| with one or more mass(es) in a file or entered manually
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	271
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	272
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	273 -----------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	274 Workflow position
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	275 -----------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	276
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	277
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	278 .. image:: ./static/images/metabolomics/hmdb.png
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	279 :width: 800
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	280
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	281
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	282 -----------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	283 Input files
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	284 -----------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	285
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	286
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	287 +-------------------------+-----------+
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	288 \| Parameter : num + label \| Format \|
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	289 +=========================+===========+
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	290 \| 1 : File of masses \| tabular \|
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	291 +-------------------------+-----------+
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	292
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	293 File of masses (Generally variable metadata file) must have at least the following column :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	294 * Masses : column with all the masses in the tsv input file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	295
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	296 ----------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	297 Parameters
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	298 ----------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	299
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	300 Would you use a file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	301 \| Choose whether the masses are in a file or entered manually
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	302 \| YES (default) : parameters File of masses ; Do you have a header ; Column of masses are visible
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	303 \| NO : parameter Mass to submit is visible
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	304 \|
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	305
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	306
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	307 If 'use file'='YES'
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	308
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	309 File of masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	310 \| see "Input files" section above
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	311 \| Tabular file format, Generally variable metadata file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	312 \|
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	313
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	314 Do you have a header
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	315 \| YES (default) : parameter Number of header lines is visible
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	316 \| NO : all lines are considered to contain masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	317 \|
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	318
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	319 If 'have a header'='YES'
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	320
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	321 Number of header lines
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	322 \| Number of lines not containing masses values, these lines will be ignored
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	323 \|
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	324
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	325 In all header cases :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	326
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	327 Column of masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	328 \| Specify the column number for the mass in the tsv input file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	329 \|
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	330
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	331
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	332 If 'use file'='NO'
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	333
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	334 Mass to submit
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	335 \| Specify a list of mass to request
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	336 \| one or more mass(es) entered manually
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	337 \| For a masses list, writes : m1 m2 m3
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	338 \| You must separate yours values with space
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	339 \| dot (.) is for float number
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	340 \|
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	341
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	342 In all cases :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	343
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	344 Mass-to-charge ratio
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	345 \| Specify a delta (mass-to-charge ratio) to apply on mass - This value is a float, between 0.0000000000000001 and 10.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	346 \|
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	347
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	348 Molecular Species
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	349 \| Type of ionization of the molecule : positif, negatif, neutral
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	350 \|
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	351
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	352
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	353 ------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	354 Output files
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	355 ------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	356
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	357 Two types of files
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	358 \| HMDB_WEB.HTML: for viewing result via HTML.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	359 \|
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	360 \| HMDB_TABULAR.tabular: for linking with others modules.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	361 \|
2 a3744fb3605c planemo upload commit e3e676478019ab709f0043c09b02ba93e042957f fgiacomoni parents: 1 diff changeset	362 \| HMDB_XLS.txt: an excel-like output permitting manual annotation cleaning.
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	363 \|
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	364
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	365 ---------------------------------------------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	366
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	367
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	368 ---------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	369 Working example
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	370 ---------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	371
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	372
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	373 .. class:: warningmark
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	374
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	375 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	376 \| Format Data For Postprocessing
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	377 \| Perform LCMS Annotations
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	378
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	379 .. class:: warningmark
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	380
24 d8e2ede293a6 Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 23 diff changeset	381 And their "W4M courses 2022":
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	382 \| Using Galaxy4Metabolomics - W4M table format for Galaxy
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	383 \| Annotation Banks - Annotation
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	384
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	385
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	386 ]]></help>
3 505956db90c5 planemo upload commit 08ff14d8ba34cbd43461ff041d4a3b8df5bbdba7 fgiacomoni parents: 2 diff changeset	387 <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel -->
505956db90c5 planemo upload commit 08ff14d8ba34cbd43461ff041d4a3b8df5bbdba7 fgiacomoni parents: 2 diff changeset	388 <citations>
505956db90c5 planemo upload commit 08ff14d8ba34cbd43461ff041d4a3b8df5bbdba7 fgiacomoni parents: 2 diff changeset	389 <citation type="doi">10.1093/nar/gks1065</citation>
14 625fa968d99a Master branch Updating - - Fxx fgiacomoni parents: 13 diff changeset	390 <citation type="doi">10.1093/nar/gkx1089</citation>
23 2d8a310e86ce Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx fgiacomoni parents: 22 diff changeset	391 <citation type="doi">10.1093/nar/gkab1062</citation>
3 505956db90c5 planemo upload commit 08ff14d8ba34cbd43461ff041d4a3b8df5bbdba7 fgiacomoni parents: 2 diff changeset	392 </citations>
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	393 </tool>

Mercurial > repos > fgiacomoni > hmdb_ms_search

annotate wsdl_hmdb.xml @ 28:6d796927335d draft