Mercurial > repos > workflow4metabolomics > xcms_refine

comparison abims_xcms_refine.xml @ 1:20f8ebc3a391 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:19:47 +0000
parents eb115eb8f25c
children
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0:eb115eb8f25c 1:20f8ebc3a391
1 <tool id="abims_xcms_refine" name="xcms refineChromPeaks (refine)" version="3.12.0+galaxy0"> 1 <tool id="abims_xcms_refine" name="xcms refineChromPeaks (refine)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 2
3 <description>Remove or merge chromatographic peaks based on specific criteria.</description> 3 <description>Remove or merge chromatographic peaks based on specific criteria.</description>
4 4
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
75 <tests> 75 <tests>
76 <!-- 76 <!--
77 test 1 - MergeNeighboringPeaks method 77 test 1 - MergeNeighboringPeaks method
78 --> 78 -->
79 <test> 79 <test>
80 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/> 80 <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
81 <conditional name="methods"> 81 <conditional name="methods">
82 <param name="method" value="MergeNeighboringPeaks"/> 82 <param name="method" value="MergeNeighboringPeaks"/>
83 <param name="expandRt" value="2" /> 83 <param name="expandRt" value="2" />
84 <param name="expandMz" value="0" /> 84 <param name="expandMz" value="0" />
85 <param name="ppm" value="10" /> 85 <param name="ppm" value="10" />
102 </test> 102 </test>
103 <!-- 103 <!--
104 test 2 - FilterIntensity method 104 test 2 - FilterIntensity method
105 --> 105 -->
106 <test> 106 <test>
107 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/> 107 <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
108 <conditional name="methods"> 108 <conditional name="methods">
109 <param name="method" value="FilterIntensity"/> 109 <param name="method" value="FilterIntensity"/>
110 <param name="threshold" value="1e5" /> 110 <param name="threshold" value="1e5" />
111 <param name="nValues" value="3" /> 111 <param name="nValues" value="3" />
112 <param name="value" value="into" /> 112 <param name="value" value="into" />
124 </test> 124 </test>
125 <!-- 125 <!--
126 test 3 - CleanPeaks method 126 test 3 - CleanPeaks method
127 --> 127 -->
128 <test> 128 <test>
129 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/> 129 <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
130 <conditional name="methods"> 130 <conditional name="methods">
131 <param name="method" value="CleanPeaks"/> 131 <param name="method" value="CleanPeaks"/>
132 <param name="maxPeakwidth" value="8" /> 132 <param name="maxPeakwidth" value="8" />
133 </conditional> 133 </conditional>
134 <expand macro="test_file_load_single"/> 134 <expand macro="test_file_load_single"/>
242 --------------------------------------------------- 242 ---------------------------------------------------
243 243
244 Changelog/News 244 Changelog/News
245 -------------- 245 --------------
246 246
247 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS 247 .. _news: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
248 248
249 249
250 **Version 3.6.1.0 - 08/02/2021** 250 **Version 3.6.1.0 - 08/02/2021**
251 251
252 - NEW: first version of tool wrapper 252 - NEW: first version of tool wrapper