Mercurial > repos > lecorguille > xcms_merge

comparison xcms_merge.xml @ 8:6b5504f877ff draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
author lecorguille
date Mon, 05 Mar 2018 04:16:12 -0500
parents dca722aecb67
children 47e953d9da82
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7:dca722aecb67 8:6b5504f877ff
27 <expand macro="input_file_load"/> 27 <expand macro="input_file_load"/>
28 </inputs> 28 </inputs>
29 29
30 <outputs> 30 <outputs>
31 <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" from_work_dir="merged.RData" /> 31 <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" from_work_dir="merged.RData" />
32 <data name="sampleMetadataOutput" format="tabular" label="xset.merged.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv">
33 <filter>not sampleMetadata</filter>
34 </data>
35 <data name="ticsRawPdf" format="pdf" label="xset.merged.xset.TICs_raw.pdf" from_work_dir="TICs.pdf" />
36 <data name="bpcsRawPdf" format="pdf" label="xset.merged.xset.BPCs_raw.pdf" from_work_dir="BICs.pdf" />
32 </outputs> 37 </outputs>
33 38
34 <tests> 39 <tests>
35 <!--<test> 40 <!-- DISABLE FOR TRAVIS
41 <test>
36 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> 42 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
37 <expand macro="test_file_load_single"/> 43 <expand macro="test_file_load_single"/>
38 <assert_stdout> 44 <assert_stdout>
39 <has_text text="object with 4 samples" /> 45 <has_text text="object with 4 samples" />
40 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" /> 46 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
41 <has_text text="Mass range: 200.1-600 m/z" /> 47 <has_text text="Mass range: 200.1-600 m/z" />
42 <has_text text="Peaks: 9251 (about 2313 per sample)" /> 48 <has_text text="Peaks: 9251 (about 2313 per sample)" />
43 <has_text text="Peak Groups: 0" /> 49 <has_text text="Peak Groups: 0" />
44 <has_text text="Sample classes: ." /> 50 <has_text text="Sample classes: ." />
45 </assert_stdout> 51 </assert_stdout>
46 </test>--> 52 <output name="sampleMetadataOutput" file="noclass.merged.sampleMetadata.tsv" />
53 </test>
54 -->
47 <test> 55 <test>
48 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> 56 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
49 <expand macro="test_file_load_single"/> 57 <expand macro="test_file_load_single"/>
50 <param name="sampleMetadata" value="sampleMetadata.tab" /> 58 <param name="sampleMetadata" value="sampleMetadata.tab" />
51 <assert_stdout> 59 <assert_stdout>
163 171
164 **Version 3.0.0.0 - 14/02/2018** 172 **Version 3.0.0.0 - 14/02/2018**
165 173
166 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods 174 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods
167 175
176 **Version 1.0.1 - 13/02/2017**
177
178 - IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file
179
168 **Version 1.0.0 - 03/02/2017** 180 **Version 1.0.0 - 03/02/2017**
169 181
170 - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group 182 - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group
171 183
172 ]]></help> 184 ]]></help>