Mercurial > repos > lecorguille > xcms_merge

comparison xcms_merge.xml @ 10:47e953d9da82 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
author lecorguille
date Thu, 08 Mar 2018 05:52:52 -0500
parents 6b5504f877ff
children 67ab853b89f3
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9:35b9bb3205d8 10:47e953d9da82
19 19
20 @COMMAND_FILE_LOAD@ 20 @COMMAND_FILE_LOAD@
21 ]]></command> 21 ]]></command>
22 22
23 <inputs> 23 <inputs>
24 <param name="images" type="data" format="rdata.xcms.raw,rdata" label="xset RData / xcms.xcmsSet file" help="output file from another xcms.xcmsSet" multiple="true" /> 24 <param name="images" type="data" format="rdata.xcms.raw,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from multiple findChromPeaks" multiple="true" />
25 <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="must contain at least one column with the sample id and one column with the sample class"/> 25 <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="must contain at least one column with the sample id and one column with the sample class"/>
26 26
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"> 32 <data name="sampleMetadataOutput" format="tabular" label="xset.merged.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv">
33 <filter>not sampleMetadata</filter> 33 <filter>not sampleMetadata</filter>
34 </data> 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" />
37 </outputs> 35 </outputs>
38 36
39 <tests> 37 <tests>
40 <!-- DISABLE FOR TRAVIS 38 <!-- DISABLE FOR TRAVIS
41 <test> 39 <test>
167 --------------------------------------------------- 165 ---------------------------------------------------
168 166
169 Changelog/News 167 Changelog/News
170 -------------- 168 --------------
171 169
172 **Version 3.0.0.0 - 14/02/2018** 170 **Version 3.0.0.0 - 08/03/2018**
173 171
174 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods 172 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods
173
174 - IMPROVMENT: a new dedicated tool "xcms plot chromatogram" will allow you to get TIC and BPI of your raw data.
175
176 - IMPROVMENT: the tool will now generate a sampleMetadata file if any was provided. It will be useful to add some further information for the normalization and statistics steps.
175 177
176 **Version 1.0.1 - 13/02/2017** 178 **Version 1.0.1 - 13/02/2017**
177 179
178 - IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file 180 - IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file
179 181