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comparison msstats.xml @ 2:52ac6fde9a5b draft

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"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
comparison
equal deleted inserted replaced
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