Mercurial > repos > fgiacomoni > hmdb_ms_search

comparison wsdl_hmdb.xml @ 14:625fa968d99a draft

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Master branch Updating - - Fxx
author fgiacomoni
date Thu, 10 Jan 2019 09:10:14 -0500
parents 3587cb923890
children beb9619263b0
comparison
equal deleted inserted replaced
13:3587cb923890 14:625fa968d99a
1 <tool id="wsdl_hmdb" name="HMDB MS search" version="2018-10-01"> 1 <tool id="wsdl_hmdb" name="HMDB MS search" version="2018-10-01">
2 <description> 2 <description>
3 search by masses on HMDB online bank 3 search by masses on HMDB online LCMS bank
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
7 <requirement type="package" version="2.161">perl-data-dumper</requirement> 7 <requirement type="package" version="2.161">perl-data-dumper</requirement>
8 <requirement type="package" version="2.97">perl-html-template</requirement> 8 <requirement type="package" version="2.97">perl-html-template</requirement>
90 <filter>input_type['choice'] == "NO"</filter> 90 <filter>input_type['choice'] == "NO"</filter>
91 </data> 91 </data>
92 </outputs> 92 </outputs>
93 93
94 <tests> 94 <tests>
95 <!-- 95 <!--test 01 no result - fake-mzrt-input-with-id -->
96 <!--
96 <test> 97 <test>
97 <!~~test 01 no result - fake-mzrt-input-with-id ~~>
98 <param name="choice" value="YES"/> 98 <param name="choice" value="YES"/>
99 <param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/> 99 <param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/>
100 <param name="header_choice" value="yes"/> 100 <param name="header_choice" value="yes"/>
101 <param name="nblineheader" value="1"/> 101 <param name="nblineheader" value="1"/>
102 <param name="colfactor" value="2"/> 102 <param name="colfactor" value="2"/>
105 <param name="maxquery" value="5"/> 105 <param name="maxquery" value="5"/>
106 <output name="variableMetadata" file="out_test01.tabular"/> 106 <output name="variableMetadata" file="out_test01.tabular"/>
107 <output name="HmdbOutWeb" file="out_test01.html"/> 107 <output name="HmdbOutWeb" file="out_test01.html"/>
108 <output name="HmdbOutXlsx" file="out_test01.txt"/> 108 <output name="HmdbOutXlsx" file="out_test01.txt"/>
109 </test> 109 </test>
110 -->
111 <!--test 02 : some results - with-mzrt-input-with-id file-->
112 <!--
110 <test> 113 <test>
111 <!~~test 02 : some results - with-mzrt-input-with-id file~~>
112 <param name="choice" value="YES"/> 114 <param name="choice" value="YES"/>
113 <param name="masses" value="input_test02_mzrt-input-with-id.tabular"/> 115 <param name="masses" value="input_test02_mzrt-input-with-id.tabular"/>
114 <param name="header_choice" value="yes"/> 116 <param name="header_choice" value="yes"/>
115 <param name="nblineheader" value="1"/> 117 <param name="nblineheader" value="1"/>
116 <param name="colfactor" value="2"/> 118 <param name="colfactor" value="2"/>
119 <param name="maxquery" value="5"/> 121 <param name="maxquery" value="5"/>
120 <output name="variableMetadata" file="out_test02.tabular"/> 122 <output name="variableMetadata" file="out_test02.tabular"/>
121 <output name="HmdbOutWeb" file="out_test02.html"/> 123 <output name="HmdbOutWeb" file="out_test02.html"/>
122 <output name="HmdbOutXlsx" file="out_test02.txt"/> 124 <output name="HmdbOutXlsx" file="out_test02.txt"/>
123 </test> 125 </test>
124 --> 126 -->
127 <!--test 03 : some results - with-mz list in manual mass mode-->
125 <test> 128 <test>
126 <!--test 03 : some results - with-mz list in manual mass mode-->
127 <param name="choice" value="NO"/> 129 <param name="choice" value="NO"/>
128 <param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/> 130 <param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/>
129 <param name="delta" value="0.05"/> 131 <param name="delta" value="0.05"/>
130 <param name="mode" value="positive"/> 132 <param name="mode" value="positive"/>
131 <param name="maxquery" value="5"/> 133 <param name="maxquery" value="5"/>
145 147
146 .. class:: infomark 148 .. class:: infomark
147 149
148 **Please cite** If you use this tool, please add the following reference 150 **Please cite** If you use this tool, please add the following reference
149 | 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. 151 | 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.
152 | 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.
150 153
151 154
152 --------------------------------------------------- 155 ---------------------------------------------------
153 156
154 ============== 157 ==============
269 | Format Data For Postprocessing 272 | Format Data For Postprocessing
270 | Perform LCMS Annotations 273 | Perform LCMS Annotations
271 274
272 .. class:: warningmark 275 .. class:: warningmark
273 276
274 And their "W4M courses 2015": 277 And their "W4M courses 2018":
275 | Using Galaxy4Metabolomics - W4M table format for Galaxy 278 | Using Galaxy4Metabolomics - W4M table format for Galaxy
276 | Annotation Banks - Annotation 279 | Annotation Banks - Annotation
277 280
278 281
279 ]]></help> 282 ]]></help>
280 <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel --> 283 <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel -->
281 <citations> 284 <citations>
282 <citation type="doi">10.1093/nar/gks1065</citation> 285 <citation type="doi">10.1093/nar/gks1065</citation>
286 <citation type="doi">10.1093/nar/gkx1089</citation>
283 </citations> 287 </citations>
284 </tool> 288 </tool>