Mercurial > repos > lecorguille > xcms_fillpeaks
comparison abims_xcms_fillPeaks.xml @ 16:34fe699200ce draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 878be1bfbe93af0a140df76fa47f0a82a48189e3
author | lecorguille |
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date | Tue, 09 Oct 2018 04:42:22 -0400 |
parents | 91c71f3808f3 |
children | b6b62413936f |
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15:1b60d8eb704a | 16:34fe699200ce |
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1 <tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.0"> | 1 <tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.1"> |
2 | 2 |
3 <description>Integrate areas of missing peaks</description> | 3 <description>Integrate areas of missing peaks</description> |
4 | 4 |
5 <macros> | 5 <macros> |
6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
35 <param argument="expandMz" type="integer" value="0" label="Value by which the mz width of peaks should be expanded" help="Each peak is expanded in mz direction by ‘expandMz *’ their original mz width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the mz width of the peak resulting in peakswith twice their original size in mz direction (expansion by half mz width to both sides)." /> | 35 <param argument="expandMz" type="integer" value="0" label="Value by which the mz width of peaks should be expanded" help="Each peak is expanded in mz direction by ‘expandMz *’ their original mz width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the mz width of the peak resulting in peakswith twice their original size in mz direction (expansion by half mz width to both sides)." /> |
36 <param argument="expandRt" type="integer" value="0" label="Value by which the RT width of peaks should be expanded" help="Each peak is expanded in RT direction by ‘expandRt *’ their original RT width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the RT width of the peak resulting in peakswith twice their original size in RT direction (expansion by half RT width to both sides)."/> | 36 <param argument="expandRt" type="integer" value="0" label="Value by which the RT width of peaks should be expanded" help="Each peak is expanded in RT direction by ‘expandRt *’ their original RT width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the RT width of the peak resulting in peakswith twice their original size in RT direction (expansion by half RT width to both sides)."/> |
37 <param argument="ppm" type="integer" value="0" label="Specifying a ppm by which the mz width of the peak region should be expanded" help="For peaks with an mz width smaller than ‘mean(c(mzmin, mzmax)) * ppm / 1e6’, the ‘mzmin’ will be replaced by ‘mean(c(mzmin, mzmax)) - (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’ and ‘mzmax’ by ‘mean(c(mzmin, mzmax)) + (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’. This is applied before eventually expanding the mz width using the ‘expandMz’ parameter." /> | 37 <param argument="ppm" type="integer" value="0" label="Specifying a ppm by which the mz width of the peak region should be expanded" help="For peaks with an mz width smaller than ‘mean(c(mzmin, mzmax)) * ppm / 1e6’, the ‘mzmin’ will be replaced by ‘mean(c(mzmin, mzmax)) - (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’ and ‘mzmax’ by ‘mean(c(mzmin, mzmax)) + (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’. This is applied before eventually expanding the mz width using the ‘expandMz’ parameter." /> |
38 </section> | 38 </section> |
39 | 39 |
40 <expand macro="input_peaklist"/> | 40 <expand macro="input_peaklist_section"/> |
41 | 41 |
42 <expand macro="input_file_load"/> | 42 <expand macro="input_file_load"/> |
43 | 43 |
44 </inputs> | 44 </inputs> |
45 | 45 |
128 <output name="variableMetadata" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv" /> | 128 <output name="variableMetadata" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv" /> |
129 <output name="dataMatrix" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.tsv" /> | 129 <output name="dataMatrix" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.tsv" /> |
130 </test>--> | 130 </test>--> |
131 <test> | 131 <test> |
132 <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData" ftype="rdata"/> | 132 <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData" ftype="rdata"/> |
133 <conditional name="peaklist"> | 133 <section name="peaklist"> |
134 <param name="peaklistBool" value="true" /> | 134 <param name="peaklistBool" value="true" /> |
135 <param name="convertRTMinute" value="false" /> | 135 <param name="convertRTMinute" value="false" /> |
136 <param name="numDigitsMZ" value="4" /> | 136 <param name="numDigitsMZ" value="4" /> |
137 <param name="numDigitsRT" value="1" /> | 137 <param name="numDigitsRT" value="1" /> |
138 </conditional> | 138 </section> |
139 <expand macro="test_file_load_single"/> | 139 <expand macro="test_file_load_single"/> |
140 <assert_stdout> | 140 <assert_stdout> |
141 <has_text text="expandMz: 0" /> | 141 <has_text text="expandMz: 0" /> |
142 <has_text text="expandRt: 0" /> | 142 <has_text text="expandRt: 0" /> |
143 <has_text text="object with 4 samples" /> | 143 <has_text text="object with 4 samples" /> |
228 --------------------------------------------------- | 228 --------------------------------------------------- |
229 | 229 |
230 Changelog/News | 230 Changelog/News |
231 -------------- | 231 -------------- |
232 | 232 |
233 **Version 3.0.0.1 - 09/10/2018** | |
234 | |
235 - IMPROVEMENT: the export of the PeakList is now mandatory | |
236 | |
237 | |
233 **Version 3.0.0.0 - 08/03/2018** | 238 **Version 3.0.0.0 - 08/03/2018** |
234 | 239 |
235 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed. | 240 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed. |
236 | 241 |
237 - UPDATE: since xcms 3.0.0, the selection of a method is no more needed (chrom or MSW). xcms will detect from the data the peak picking method used in findChromPeaks | 242 - UPDATE: since xcms 3.0.0, the selection of a method is no more needed (chrom or MSW). xcms will detect from the data the peak picking method used in findChromPeaks |