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comparison wsdl_lipidmaps.xml @ 2:1276908e8fc4 draft

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Master branch Updating - - Fxx
author fgiacomoni
date Mon, 20 Aug 2018 09:17:05 -0400
parents e8bd49794291
children f4e6b77c46e3
comparison
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1:adf9ae010b1c 2:1276908e8fc4
1 <tool id="lipidmaps" name="Lipidmaps " version="2016-09-27"> 1 <tool id="lipidmaps" name="Lipidmaps " version="2018-08-20">
2 <description> 2 <description>
3 : search on LIPID MAPS Structure Database (LMSD) online with masses and its Text/Ontology-based search engine. 3 : search on LIPID MAPS Structure Database (LMSD) online with masses and its Text/Ontology-based search engine.
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="0.413">perl-list-moreutils</requirement> 6 <requirement type="package" version="0.413">perl-list-moreutils</requirement>
29 29
30 #if str($data_type.modify_data_action) == "yes" : 30 #if str($data_type.modify_data_action) == "yes" :
31 -listneutralloss ${data_type.neutral_loss} -listoxidation ${data_type.oxidation} 31 -listneutralloss ${data_type.neutral_loss} -listoxidation ${data_type.oxidation}
32 #end if 32 #end if
33 33
34 -output $variableMetadata_out -view $LMSDOutWeb 34 -output $variableMetadata_out -view $LMSDOutWeb -summary $LMSDOutSum
35 35
36 ]]></command> 36 ]]></command>
37 <inputs> 37 <inputs>
38 <param name="file_input" label="File of masses (Variable Metadata) " format="tabular" type="data" help="A tabular/csv file is needed and can contains a header line."/> 38 <param name="file_input" label="File of masses (Variable Metadata) " format="tabular" type="data" help="A tabular/csv file is needed and can contains a header line."/>
39 <param name="lineheader" label="Number of header lines " type="integer" value="0" size="10" help="number of lines not containing values"/> 39 <param name="lineheader" label="Number of header lines " type="integer" value="0" size="10" help="number of lines not containing values"/>
1639 <param name="tolerance" label="Mass-to-charge ratio " type="float" min="0" max="100" value="0.5" size="10" help="Default value is 0.5 for LM (mass-to-charge ratio)" /> 1639 <param name="tolerance" label="Mass-to-charge ratio " type="float" min="0" max="100" value="0.5" size="10" help="Default value is 0.5 for LM (mass-to-charge ratio)" />
1640 </inputs> 1640 </inputs>
1641 <outputs> 1641 <outputs>
1642 <data name="variableMetadata_out" format="tabular" label="${file_input.name[:-6]}.LMSD.tabular"/> 1642 <data name="variableMetadata_out" format="tabular" label="${file_input.name[:-6]}.LMSD.tabular"/>
1643 <data name="LMSDOutWeb" format="html" label="${file_input.name[:-6]}.LMSD_WEB.html"/> 1643 <data name="LMSDOutWeb" format="html" label="${file_input.name[:-6]}.LMSD_WEB.html"/>
1644 <data name="LMSDOutSum" format="tabular" label="${file_input.name[:-6]}.LMSD_SUM.tabular"/>
1644 </outputs> 1645 </outputs>
1645 <tests> 1646 <tests>
1646 <test> 1647 <test>
1647 <!--test 01 some results - input01_50_without_class.csv --> 1648 <!--test 01 some results - input01_50_without_class.csv -->
1648 <param name="file_input" value="input01_50_without_class.csv"/> 1649 <param name="file_input" value="input01_50_without_class.csv"/>
1656 <param name="filter_cat" value="3"/> 1657 <param name="filter_cat" value="3"/>
1657 <param name="filter_class" value="306"/> 1658 <param name="filter_class" value="306"/>
1658 <param name="filter_subclass" value="NA_306"/> 1659 <param name="filter_subclass" value="NA_306"/>
1659 <output name="variableMetadata_out" file="out_test01.tabular"/> 1660 <output name="variableMetadata_out" file="out_test01.tabular"/>
1660 <output name="LMSDOutWeb" file="out_test01.html"/> 1661 <output name="LMSDOutWeb" file="out_test01.html"/>
1662 <output name="LMSDOutSum" file="out_sum_test01.tabular"/>
1661 </test> 1663 </test>
1662 <test> 1664 <test>
1663 <!--test 02 : some results - input02_480_several_class.csv file--> 1665 <!--test 02 : some results - input02_480_several_class.csv file-->
1664 <param name="file_input" value="input02_480_several_class.csv"/> 1666 <param name="file_input" value="input02_480_several_class.csv"/>
1665 <param name="mode" value="NEU"/> 1667 <param name="mode" value="NEU"/>
1670 <param name="round_type" value="round"/> 1672 <param name="round_type" value="round"/>
1671 <param name="complex_query_action" value="yes"/> 1673 <param name="complex_query_action" value="yes"/>
1672 <param name="col_classif_id" value="3"/> 1674 <param name="col_classif_id" value="3"/>
1673 <output name="variableMetadata_out" file="out_test02.tabular"/> 1675 <output name="variableMetadata_out" file="out_test02.tabular"/>
1674 <output name="LMSDOutWeb" file="out_test02.html"/> 1676 <output name="LMSDOutWeb" file="out_test02.html"/>
1677 <output name="LMSDOutSum" file="out_sum_test02.tabular"/>
1675 </test> 1678 </test>
1676 <test> 1679 <test>
1677 <!--test 03 : some results - input03_200_without_class_on_maincl_301.csv file--> 1680 <!--test 03 : some results - input03_200_without_class_on_maincl_301.csv file-->
1678 <param name="file_input" value="input03_200_without_class_on_maincl_301.csv"/> 1681 <param name="file_input" value="input03_200_without_class_on_maincl_301.csv"/>
1679 <param name="mode" value="NEU"/> 1682 <param name="mode" value="NEU"/>
1686 <param name="tolerance" value="0.5"/> 1689 <param name="tolerance" value="0.5"/>
1687 <param name="decimal" value="2"/> 1690 <param name="decimal" value="2"/>
1688 <param name="round_type" value="round"/> 1691 <param name="round_type" value="round"/>
1689 <output name="variableMetadata_out" file="out_test03.tabular"/> 1692 <output name="variableMetadata_out" file="out_test03.tabular"/>
1690 <output name="LMSDOutWeb" file="out_test03.html"/> 1693 <output name="LMSDOutWeb" file="out_test03.html"/>
1694 <output name="LMSDOutSum" file="out_sum_test03.tabular"/>
1691 </test> 1695 </test>
1692 <test> 1696 <test>
1693 <!--test 04 some results and mz transfo with the mode - input01_50_without_class.csv --> 1697 <!--test 04 some results and mz transfo with the mode - input01_50_without_class.csv -->
1694 <param name="file_input" value="input01_50_without_class.csv"/> 1698 <param name="file_input" value="input01_50_without_class.csv"/>
1695 <param name="mode" value="POS"/> 1699 <param name="mode" value="POS"/>
1702 <param name="filter_cat" value="3"/> 1706 <param name="filter_cat" value="3"/>
1703 <param name="filter_class" value="306"/> 1707 <param name="filter_class" value="306"/>
1704 <param name="filter_subclass" value="NA_306"/> 1708 <param name="filter_subclass" value="NA_306"/>
1705 <output name="variableMetadata_out" file="out_test04.tabular"/> 1709 <output name="variableMetadata_out" file="out_test04.tabular"/>
1706 <output name="LMSDOutWeb" file="out_test04.html"/> 1710 <output name="LMSDOutWeb" file="out_test04.html"/>
1711 <output name="LMSDOutSum" file="out_sum_test04.tabular"/>
1707 </test> 1712 </test>
1708 </tests> 1713 </tests>
1709 <help><![CDATA[ 1714 <help><![CDATA[
1710 1715
1711 .. class:: infomark 1716 .. class:: infomark
1815 1820
1816 Two types of files 1821 Two types of files
1817 1822
1818 | LMSD_WEB.html: for viewing result via HTML. 1823 | LMSD_WEB.html: for viewing result via HTML.
1819 | LMSD.tabular: for linking with others modules. 1824 | LMSD.tabular: for linking with others modules.
1825 | LMSD_SUM.tabular: for summary result by cluster - NEW.
1820 1826
1821 1827
1822 --------------- 1828 ---------------
1823 Working example 1829 Working example
1824 --------------- 1830 ---------------