Mercurial > repos > galaxyp > msstats
comparison msstats.xml @ 2:52ac6fde9a5b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 414edbbd89f9bc83b81289e409c9b688c8c1e40f"
| author | galaxyp |
|---|---|
| date | Fri, 14 Aug 2020 12:19:14 -0400 |
| parents | 3e2606fa85bf |
| children | 8212e342e482 |
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| 1:3e2606fa85bf | 2:52ac6fde9a5b |
|---|---|
| 230 width=5, height=5, address="MSStats_group_") | 230 width=5, height=5, address="MSStats_group_") |
| 231 #end if | 231 #end if |
| 232 | 232 |
| 233 #if 'volcanoplot' in $group.select_outputs | 233 #if 'volcanoplot' in $group.select_outputs |
| 234 \# volcano plot | 234 \# volcano plot |
| 235 groupComparisonPlots(data = comparisons\$ComparisonResult, type = 'VolcanoPlot', | 235 groupComparisonPlots(data = comparisons\$ComparisonResult, type = 'VolcanoPlot',ProteinName=FALSE, |
| 236 width=5, height=5, address="MSStats_group_") | 236 width=5, height=5, address="MSStats_group_") |
| 237 #end if | 237 #end if |
| 238 | 238 |
| 239 #if 'heatmap' in $group.select_outputs | 239 #if 'heatmap' in $group.select_outputs |
| 240 \# heatmap - works only for more than 1 comparison | 240 \# heatmap - works only for more than 1 comparison |
| 702 ... ... ... ... ... | 702 ... ... ... ... ... |
| 703 | 703 |
| 704 | 704 |
| 705 - Annotations as tabular file are needed for all input options except MSstats format | 705 - Annotations as tabular file are needed for all input options except MSstats format |
| 706 | 706 |
| 707 - 4 columns: Filename, Condition, Bioreplicate, Run; additional 5th column only for MaxQuant: Isotopelabeltype | 707 - 4 columns with exactly these headers: Raw.file, Condition, BioReplicate, Run; additional 5th column only for MaxQuant: IsotopeLabelType |
| 708 | 708 |
| 709 - Filename: the file name has to be exactly as it appears in the other input files (e.g. S1207.raw.thermo; in/AA12_mzML.mzML) | 709 - Raw.file: File name that has to match exactly as it appears in the other input files (e.g. S1207.raw.thermo; in/AA12_mzML.mzML) |
| 710 - all other columns: see description above for MSstats format columns | 710 - all other columns: see description above for MSstats format columns |
| 711 | 711 |
| 712 - Comparison matrix as tabular file | 712 - Comparison matrix as tabular file |
| 713 | 713 |
| 714 - 1st column: name of comparison | 714 - 1st column: name of comparison |