Mercurial > repos > lecorguille > xcms_plot_chromatogram

comparison xcms_plot_chromatogram.xml @ 10:dbd877060ac3 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author workflow4metabolomics
date Wed, 12 Feb 2020 08:30:06 -0500
parents 0290cd6b3354
children 37d31fd64eb4
comparison
equal deleted inserted replaced
9:271c9d5f0d10 10:dbd877060ac3
1 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@WRAPPER_VERSION@.0"> 1 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@TOOL_VERSION@.0">
2 <description>Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s)</description> 2 <description>Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s)</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <import>macros_xcms.xml</import> 6 <import>macros_xcms.xml</import>
7 </macros> 7 </macros>
8
9 <expand macro="requirements"/> 8 <expand macro="requirements"/>
10 <expand macro="stdio"/> 9 <expand macro="stdio"/>
11 10
12 <command><![CDATA[ 11 <command><![CDATA[
13 @COMMAND_RSCRIPT@//xcms_plot_chromatogram.r 12 @COMMAND_RSCRIPT@//xcms_plot_chromatogram.r
36 <tests> 35 <tests>
37 <test> 36 <test>
38 <param name="images" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/> 37 <param name="images" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
39 <expand macro="test_file_load_single"/> 38 <expand macro="test_file_load_single"/>
40 <param name="sampleMetadata" value="sampleMetadata.tab" ftype="tabular"/> 39 <param name="sampleMetadata" value="sampleMetadata.tab" ftype="tabular"/>
41 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" /> 40 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="5000" />
42 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" /> 41 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="5000" />
43 </test> 42 </test>
44 <!-- DISABLE FOR TRAVIS 43 <!-- DISABLE FOR TRAVIS
45 <test> 44 <test>
46 <param name="images" value="ko15-raw.RData,ko16-raw.RData,wt15-raw.RData,wt16-raw.RData" ftype="rdata"/> 45 <param name="images" value="ko15-raw.RData,ko16-raw.RData,wt15-raw.RData,wt16-raw.RData" ftype="rdata"/>
47 <expand macro="test_file_load_single"/> 46 <expand macro="test_file_load_single"/>
103 Changelog/News 102 Changelog/News
104 -------------- 103 --------------
105 104
106 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS 105 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
107 106
108 **Version 3.4.4.0 - 08/02/2019** 107 @HELP_XCMS_NEWVERSION_3610@
109 108
110 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) 109 @HELP_XCMS_NEWVERSION_3440@
111 110
112 **Version 3.0.0.0 - 07/03/2018** 111 **Version 3.0.0.0 - 07/03/2018**
113 112
114 - NEW: This new tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience. It will replace those created by xcmsSet and retcor tools. 113 - NEW: This new tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience. It will replace those created by xcmsSet and retcor tools.
115 114