msstatstmt: msstatstmt.xml annotate

annotate msstatstmt.xml @ 1:b79d4c961009 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 5ac4f6093606746adb0d40fe4f73871f5934d091"

author	galaxyp
date	Fri, 05 Feb 2021 18:42:55 +0000
parents	fd3dc69b78ff
children	782bd55b000b

rev	line source
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	1 <tool id="msstatstmt" name="MSstatsTMT" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	2 <description>protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</description>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	3 <macros>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	4 <token name="@TOOL_VERSION@">1.8.0</token>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	5 <token name="@GALAXY_VERSION@">0</token>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	6 <xml name="input_options_shared">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	7 <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use unique peptide" help="Yes (default) removes peptides that are assigned for more than one protein. We assume to use unique peptide for each protein." />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	8 <param name="rmPSM_withMissing_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove PSM with missing value within run" help="Yes will remove PSM with any missing value within each run. Default is No." />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	9 <param name="rmPSM_withfewMea_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove PSM with few measurements within run" help="Only for 'Remove PSM with missing value within run = No'. Yes (default) will remove the features that have 1 or 2 measurements within each run." />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	10 <param name="rmProtein_with1Feature" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove proteins with one feature" help="Yes will remove the proteins which have only 1 peptide and charge. Default is No." />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	11 </xml>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	12 </macros>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	13 <requirements>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	14 <requirement type="package" version="@TOOL_VERSION@">bioconductor-msstatstmt</requirement>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	15 </requirements>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	16 <command detect_errors="exit_code"><![CDATA[
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	17 cat '$msstatstmt_script' > '$out_r_script' &&
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	18 Rscript '$msstatstmt_script'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	19 && cat msstats*.log > '$out_msstats_log'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	20 && cat msstatstmt.log > '$out_msstatstmt_log'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	21 ]]></command>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	22 <configfiles>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	23 <configfile name="msstatstmt_script"><![CDATA[
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	24 library(MSstatsTMT, warn.conflicts = F, quietly = T, verbose = F)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	25
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	26 #if $input.input_src == 'MSstatsTMT'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	27 input <- read.table("$input.msstatstmt_input", sep="\t", header=TRUE)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	28
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	29 #elif $input.input_src == 'MaxQuant'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	30 proteinGroups.mq <- read.table("$input.proteinGroups", sep="\t", header=TRUE)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	31 evidence.mq <- read.table("$input.evidence", sep="\t", header=TRUE)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	32 annotation.mq <- read.table("$input.annotation", sep="\t", header=TRUE)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	33
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	34 input <- MaxQtoMSstatsTMTFormat(evidence = evidence.mq,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	35 proteinGroups = proteinGroups.mq,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	36 annotation = annotation.mq,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	37 which.proteinid = "$input.proteinID",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	38 rmProt_Only.identified.by.site = $input.input_options.rmProt_Onlyidentifiedbysite,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	39 useUniquePeptide = $input.input_options.useUniquePeptide,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	40 rmPSM_withMissing_withinRun = $input.input_options.rmPSM_withMissing_withinRun,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	41 rmPSM_withfewMea_withinRun = $input.input_options.rmPSM_withfewMea_withinRun,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	42 rmProtein_with1Feature = $input.input_options.rmProtein_with1Feature,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	43 summaryforMultipleRows = $input.input_options.summaryforMultipleRows)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	44
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	45 #elif $input.input_src == 'OpenMS'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	46 input.oms <- read.table("$input.oms_input", sep="\t", header=TRUE)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	47
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	48 input <- OpenMStoMSstatsTMTFormat(input.oms,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	49 useUniquePeptide = $input.input_options.useUniquePeptide,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	50 rmPSM_withMissing_withinRun = $input.input_options.rmPSM_withMissing_withinRun,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	51 rmPSM_withfewMea_withinRun = $input.input_options.rmPSM_withfewMea_withinRun,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	52 rmProtein_with1Feature = $input.input_options.rmProtein_with1Feature,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	53 summaryforMultiplePSMs = $input.input_options.summaryforMultiplePSMs)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	54 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	55
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	56 quant <- proteinSummarization(input,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	57 method = "$proteinSummarization.method",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	58 global_norm = $proteinSummarization.global_norm,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	59 reference_norm = $proteinSummarization.reference_norm,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	60 remove_norm_channel = $proteinSummarization.remove_norm_channel,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	61 remove_empty_channel = $proteinSummarization.remove_empty_channel,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	62 MBimpute = $proteinSummarization.MBimpute,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	63 #if $proteinSummarization.maxQuantileforCensored == ''
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	64 maxQuantileforCensored = NULL)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	65 #else
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	66 maxQuantileforCensored = $proteinSummarization.maxQuantileforCensored)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	67 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	68
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	69 #for $plot_type in $selected_outputs
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	70 #if $plot_type[-4:] == "Plot"
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	71 dataProcessPlotsTMT(input,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	72 quant,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	73 type = '$plot_type',
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	74 ylimUp = $out_plots_opt.ylimUp,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	75 ylimDown = $out_plots_opt.ylimDown,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	76 x.axis.size = $out_plots_opt.x_axis_size,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	77 y.axis.size = $out_plots_opt.y_axis_size,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	78 text.size = $out_plots_opt.text_size,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	79 text.angle = $out_plots_opt.text_angle,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	80 legend.size = $out_plots_opt.legend_size,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	81 dot.size.profile = $out_plots_opt.dot_size_profile,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	82 ncol.guide = $out_plots_opt.ncol_guide,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	83 width = $out_plots_opt.width,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	84 height = $out_plots_opt.height,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	85 #if $out_plots_opt.which_Protein.select != 'list'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	86 which.Protein = "$out_plots_opt.which_Protein.select",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	87 #else
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	88 which.Protein = unlist(read.table("$out_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE),
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	89 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	90 originalPlot = $out_plots_opt.originalPlot,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	91 summaryPlot = $out_plots_opt.summaryPlot)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	92 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	93 #end for
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	94
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	95 #if $group.group_comparison == 'true'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	96 #if $group.use_comp_matrix.select == 'true'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	97 comp_matrix <- read.table("$group.use_comp_matrix.comparison_matrix", sep="\t", header=TRUE, check.names=FALSE)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	98
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	99 comparison <- comp_matrix[,-1]
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	100 row.names(comparison) <- as.character(comp_matrix[,1])
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	101 comparison <- as.matrix(comparison[levels(quant\$Condition)])
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	102 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	103
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	104 comparisons <- groupComparisonTMT(data = quant,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	105 #if $group.use_comp_matrix.select == 'true'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	106 contrast.matrix = comparison,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	107 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	108 moderated = $group.moderated,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	109 adj.method = "$group.adj_method",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	110 remove_norm_channel = $group.remove_norm_channel,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	111 remove_empty_channel = $group.remove_empty_channel)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	112
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	113 write.table(comparisons,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	114 "ComparisonResult.tsv",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	115 sep = "\t",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	116 quote = F,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	117 row.names = F,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	118 dec = ".")
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	119 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	120 ]]></configfile>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	121 </configfiles>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	122 <inputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	123 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	124 <param name="input_src" type="select" label="Input Source">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	125 <option value="MSstatsTMT">MStatsTMT (11 column format)</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	126 <option value="MaxQuant">MaxQuant</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	127 <option value="OpenMS">OpenMS</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	128 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	129 <when value="MSstatsTMT">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	130 <param name="msstatstmt_input" type="data" format="tabular" label="MStatsTMT (11 column format)"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	131 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	132 <when value="MaxQuant">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	133 <param name="evidence" type="data" format="tabular" label="evidence.txt - feature-level data"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	134 <param name="proteinGroups" type="data" format="tabular" label="proteinGroups.txt" help="It needs to matching protein group ID. If proteinGroups=NULL, use 'Proteins' column in 'evidence.txt'"/>
1 b79d4c961009 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 5ac4f6093606746adb0d40fe4f73871f5934d091" galaxyp parents: 0 diff changeset	135 <param name="annotation" type="data" format="tabular" label="annotation.txt" help="Data frame which contains column Run, Fraction, TechRepMixture, Channel, Condition, BioReplicate, Mixture." />
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	136 <param name="proteinID" type="select" label="Select Protein ID in evidence.txt">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	137 <option value="Proteins">Protein column</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	138 <option value="Leading.razor.protein">Leading razor protein column</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	139 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	140 <section name="input_options" title="MaxQtoMSstatsTMTFormat Options" expanded="false">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	141 <param name="rmProt_Onlyidentifiedbysite" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove proteins only identified by site" help="Yes will remove proteins with ’+’ in ’Only.identified.by.site’ column from proteinGroups.txt, which was identified only by a modification site. No is the default." />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	142 <expand macro="input_options_shared"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	143 <param name="summaryforMultipleRows" type="select" label="Summary for multiple rows" help="When there are multiple measurements for certain feature in certain run, select the feature with the largest summation or maximal value.">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	144 <option value="max">max</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	145 <option value="sum" selected="true">sum</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	146 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	147 </section>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	148 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	149 <when value="OpenMS">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	150 <param name="oms_input" type="data" format="tabular" label="OpenMS input"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	151 <section name="input_options" title="OpenMStoMSstatsTMTFormat Options" expanded="false">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	152 <expand macro="input_options_shared"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	153 <param name="summaryforMultiplePSMs" type="select" label="Summary for multiple PSMs" help="When there are multiple measurements for certain feature in certain run, select the feature with the largest summation or maximal value.">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	154 <option value="max">max</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	155 <option value="sum" selected="true">sum</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	156 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	157 </section>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	158 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	159 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	160 <section name="proteinSummarization" title="proteinSummarization Options" expanded="false">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	161 <param name="method" type="select" multiple="false" label="Select method">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	162 <option value="msstats" selected="true">msstats</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	163 <option value="MedianPolish">MedianPolish</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	164 <option value="Median">Median</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	165 <option value="LogSum">LogSum</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	166 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	167 <param name="global_norm" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Global median normalization" help="Global median normalization on peptide level data (equalizing the medians across all the channels and MS runs). Default is Yes. It will be performed before protein-level summarization."/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	168 <param name="reference_norm" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Reference channel based normalization" help="Reference channel based normalization between MS runs on protein level data. Yes (default) needs at least one reference channel in each MS run, annotated by ’Norm’ in condition column. It will be performed after protein-level summarization. No will not perform this normalization step. If data only has one run, then use No"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	169 <param name="remove_norm_channel" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove ’Norm’ channels from protein level data."/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	170 <param name="remove_empty_channel" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove ’Empty’ channels from protein level data"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	171 <param name="MBimpute" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="MBimpute" help="Only for 'method = msstats'. Yes (default) imputes missing values by accelerated failure time (AFT) model. No uses minimum value to impute the missing value for each peptide precursor ion."/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	172 <param name="maxQuantileforCensored" type="float" optional="true" min="0" max="0.999" value="" label="Maximum quantile for deciding censored missing value" help="We assume missing values are censored. maxQuantileforCensored is maximum quantile for deciding censored missing value, for instance, 0.999. Default is empty"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	173 </section>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	174 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	175 <param name="group_comparison" type="select" label="Compare Groups">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	176 <option value="false">No</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	177 <option value="true">Yes</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	178 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	179 <when value="false"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	180 <when value="true">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	181 <conditional name="use_comp_matrix">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	182 <param name="select" type="select" label="Use comparison matrix?">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	183 <option value="false">No</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	184 <option value="true">Yes</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	185 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	186 <when value="false"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	187 <when value="true">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	188 <param name="comparison_matrix" type="data" format="tabular" label="Comparison Matrix"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	189 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	190 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	191 <param name="moderated" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Moderate t statistic" help="No (default) uses ordinary t statistic"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	192 <param name="adj_method" type="select" label="Adjusted p value method for multiple comparison">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	193 <option value="holm">holm</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	194 <option value="hochberg">hochberg</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	195 <option value="hommel">hommel</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	196 <option value="bonferroni">bonferroni</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	197 <option value="BH" selected="true">BH</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	198 <option value="BY">BY</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	199 <option value="fdr">fdr</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	200 <option value="none">none</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	201 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	202 <param name="remove_norm_channel" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove ’Norm’ channels from protein level data"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	203 <param name="remove_empty_channel" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove ’Empty’ channels from protein level data"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	204 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	205 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	206 <param name="selected_outputs" type="select" multiple="true" optional="false" label="Select Outputs">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	207 <option value="msstats_log" selected="true">MSstats log</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	208 <option value="msstatstmt_log" selected="true">MSstatsTMT log</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	209 <option value="r_script" selected="false">MSstats Rscript</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	210 <option value="ProfilePlot" selected="false">Profile Plot</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	211 <option value="QCPlot" selected="false">QC Plot</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	212 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	213 <section name="out_plots_opt" title="Plot Output Options" expanded="false">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	214 <param name="ylimUp" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Upper limit for y-axis in the log scale" help="No (Default) for Profile Plot and QC Plot uses the upper limit as rounded off maximum of log2(intensities) after normalization + 3."/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	215 <param name="ylimDown" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Lower limit for y-axis in the log scale" help="No (Default) for Profile Plot and QCPlot uses 0."/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	216 <param name="x_axis_size" type="integer" min="1" value="10" label="Size of x-axis labeling"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	217 <param name="y_axis_size" type="integer" min="1" value="10" label="Size of y-axis labeling"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	218 <param name="text_size" type="integer" min="1" value="4" label="Size of labels represented each condition at the top"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	219 <param name="text_angle" type="integer" min="0" max="360" value="90" label="Angle of labels represented each condition at the top"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	220 <param name="legend_size" type="integer" min="1" value="7" label="Size of legend above Profile plot"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	221 <param name="dot_size_profile" type="integer" min="1" value="2" label="Size of dots in Profile plot"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	222 <param name="ncol_guide" type="integer" min="1" value="5" label="Number of columns for legends at the top of plot"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	223 <param name="width" type="integer" min="1" value="10" label="Width of the saved pdf file"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	224 <param name="height" type="integer" min="1" value="10" label="Height of the saved pdf file"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	225 <conditional name="which_Protein">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	226 <param name="select" type="select" label="Select protein IDs to draw plots">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	227 <option value="all" selected="true">generate all plots for each protein</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	228 <option value="allonly">Option for QC plot: "allonly" will generate one QC plot with all proteins</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	229 <option value="list">Protein IDs as tabular input</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	230 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	231 <when value="all"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	232 <when value="allonly"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	233 <when value="list">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	234 <param name="protein_list" type="data" format="tabular" label="List of proteins"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	235 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	236 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	237 <param name="originalPlot" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Draw original profile plots without normalization"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	238 <param name="summaryPlot" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Draw profile plots with protein summarization for each channel and MS run"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	239 </section>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	240 </inputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	241 <outputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	242 <data name="out_msstats_log" format="txt" label="${tool.name} on ${on_string}: MSstats log">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	243 <filter>'msstats_log' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	244 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	245 <data name="out_msstatstmt_log" format="txt" label="${tool.name} on ${on_string}: MSstatsTMT log">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	246 <filter>'msstatstmt_log' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	247 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	248 <data name="out_r_script" format="txt" label="${tool.name} on ${on_string}: Rscript">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	249 <filter>'r_script' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	250 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	251 <data name="out_profile_plot" from_work_dir="ProfilePlot.pdf" format="pdf" label="${tool.name} on ${on_string}: Profile Plot">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	252 <filter>'ProfilePlot' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	253 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	254 <data name="out_qc_plot" from_work_dir="QCPlot.pdf" format="pdf" label="${tool.name} on ${on_string}: QC Plot">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	255 <filter>'QCPlot' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	256 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	257 <data name="out_group_comp" from_work_dir="ComparisonResult.tsv" format="tsv" label="${tool.name} on ${on_string}: Group Comparison">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	258 <filter>group['group_comparison'] == 'true'</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	259 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	260 </outputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	261 <tests>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	262 <test expect_num_outputs="5">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	263 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	264 <param name="input_src" value="MSstatsTMT"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	265 <param name="msstatstmt_input" ftype="tabular" value="input.msstatstmt.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	266 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	267 <param name="selected_outputs" value="msstats_log,msstatstmt_log,r_script,ProfilePlot,QCPlot"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	268 <output name="out_msstats_log">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	269 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	270 <has_text text="1 level of Isotope type labeling in this experiment" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	271 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	272 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	273 <output name="out_msstatstmt_log">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	274 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	275 <has_text text="MSstatsTMT - proteinSummarization function" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	276 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	277 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	278 <output name="out_r_script">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	279 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	280 <has_n_lines n="51" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	281 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	282 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	283 <output name="out_profile_plot" file="ProfilePlot.pdf" compare="sim_size"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	284 <output name="out_qc_plot" file="QCPlot.pdf" compare="sim_size"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	285 </test>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	286 <test expect_num_outputs="2">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	287 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	288 <param name="input_src" value="MaxQuant"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	289 <param name="evidence" ftype="tabular" value="evidence.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	290 <param name="annotation" ftype="tabular" value="annotation.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	291 <param name="proteinGroups" ftype="tabular" value="proteinGroups.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	292 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	293 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	294 <param name="group_comparison" value="true"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	295 <conditional name="use_comp_matrix">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	296 <param name="select" value="true"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	297 <param name="comparison_matrix" ftype="tabular" value="comparison_matrix.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	298 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	299 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	300 <param name="selected_outputs" value="ProfilePlot"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	301 <conditional name="which_Protein">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	302 <param name="select" value="list"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	303 <param name="protein_list" ftype="tabular" value="proteinIDs.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	304 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	305 <output name="out_group_comp">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	306 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	307 <has_n_lines n="21" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	308 <has_n_columns n="8" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	309 <has_text text="A0AVT1" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	310 <has_text text="A0AVT1" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	311 <has_text text="O43324" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	312 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	313 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	314 <output name="out_profile_plot" file="ProfilePlot_list.pdf" compare="sim_size"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	315 </test>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	316 <test expect_num_outputs="2">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	317 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	318 <param name="input_src" value="OpenMS"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	319 <param name="oms_input" ftype="tabular" value="input.oms.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	320 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	321 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	322 <param name="group_comparison" value="true"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	323 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	324 <param name="selected_outputs" value="msstats_log"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	325 <output name="out_group_comp">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	326 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	327 <has_n_lines n="51" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	328 <has_n_columns n="8" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	329 <has_text text="Long_LF-Short_HF" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	330 <has_text text="sp\|O35226\|PSMD4_MOUSE" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	331 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	332 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	333 </test>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	334 </tests>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	335 <help><![CDATA[
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	336 MSstatsTMT is an R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It is applicable to isobaric labeling quantitative proteomics, including iTRAQ and TMT data. MSstatsTMT provides functionalities for two types of analysis: 1) Protein summarization based on peptide quantification data and visualization; 2) Model-based group comparison to detect significant changes in abundance.
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	337
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	338 Notes
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	339
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	340 - MSstatsTMT 11 column format: For TMT datasets an additional 'Channel' column is required.
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	341
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	342 ::
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	343
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	344 #> ProteinName PeptideSequence
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	345 #> 1 sp\|Q60854\|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	346 #> 2 sp\|Q60854\|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	347 #> 3 sp\|Q60854\|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	348 #> 4 sp\|Q60854\|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	349 #> 5 sp\|Q60854\|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	350 #> 6 sp\|Q60854\|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	351 #> PrecursorCharge PSM Mixture
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	352 #> 1 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	353 #> 2 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	354 #> 3 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	355 #> 4 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	356 #> 5 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	357 #> 6 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	358 #> TechRepMixture Run Channel BioReplicate Condition Intensity
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	359 #> 1 3_3 3_3_3 1 21 Long_HF NA
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	360 #> 2 3_3 3_3_3 2 22 Norm 1068.580
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	361 #> 3 3_3 3_3_3 3 23 Long_M 1508.330
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	362 #> 4 3_3 3_3_3 4 24 Long_HF NA
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	363 #> 5 3_3 3_3_3 5 25 Long_LF 1580.951
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	364 #> 6 3_3 3_3_3 6 26 Long_HF 1820.072
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	365
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	366 For more information please visit the `MSstatsConvert documentation <https://bioconductor.org/packages/devel/bioc/vignettes/MSstatsConvert/inst/doc/msstats_data_format.html>`_
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	367
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	368 - Comparison matrix as tabular file
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	369
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	370 - 1st column: name of comparison
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	371 - additionally one column for each condition that is present in the tabular file. Use 1 and -1 to indicate the conditions to compare and 0 for conditions that are not compared. Multiple groups can be combined by using 0.5.
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	372 - first row contains the names of the groups, they must exactly match the condition name used in the annotation file
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	373 - each additional row represents one comparison
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	374 - Example for a two group comparison
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	375
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	376 ::
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	377
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	378 names groupA groupB
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	379 groupA-groupB 1 -1
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	380
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	381
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	382 - Example for an experiment with 5 groups and 4 different comparisons
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	383
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	384 ::
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	385
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	386 names G1 G2 G3 G4 G5
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	387 G2-G1 -1 1 0 0 0
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	388 G4-G5 0 0 0 1 -1
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	389 G3-G5 0 0 -1 0 1
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	390 G1+G2-G5 0.5 0.5 0 0 -1
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	391
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	392 For additional help please visit the `MSstatsTMT documentation <https://msstats.org/msstatstmt/>`_
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	393 ]]>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	394 </help>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	395 <citations>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	396 <citation type="doi">10.1074/mcp.ra120.002105</citation>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	397 </citations>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	398 </tool>

Mercurial > repos > galaxyp > msstatstmt

annotate msstatstmt.xml @ 1:b79d4c961009 draft