msstatstmt: msstatstmt.xml annotate

annotate msstatstmt.xml @ 2:782bd55b000b draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"

author	galaxyp
date	Sat, 27 Feb 2021 10:54:25 +0000
parents	b79d4c961009
children	5667ff6f7a40

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>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	4 <token name="@TOOL_VERSION@">1.8.2</token>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	5 <token name="@GALAXY_VERSION@">1</token>
0 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)
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	25 library(MSstats)
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	26
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	27 #if $input.input_src == 'MSstatsTMT'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	28 input <- read.table("$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	29
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	30 #elif $input.input_src == 'MaxQuant'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	31 proteinGroups.mq <- read.table("$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	32 evidence.mq <- read.table("$input.evidence", sep="\t", header=TRUE)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	33 annotation.mq <- read.table("$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	34
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	35 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	36 proteinGroups = proteinGroups.mq,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	37 annotation = annotation.mq,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	38 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	39 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	40 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	41 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	42 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	43 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	44 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	45
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	46 #elif $input.input_src == 'OpenMS'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	47 input.oms <- read.table("$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	48
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	49 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	50 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	51 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	52 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	53 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	54 summaryforMultiplePSMs = $input.input_options.summaryforMultiplePSMs)
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	55
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	56 #elif $input.input_src == 'PD'
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	57 PSM.pd <- read.table("$input.PSM", sep="\t", header=TRUE)
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	58 annotation.pd <- read.table("$input.annotation", sep="\t", header=TRUE)
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	59
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	60 input <- PDtoMSstatsTMTFormat(PSM.pd,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	61 annotation = annotation.pd,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	62 which.proteinid = "$input.proteinID",
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	63 useNumProteinsColumn = $input.input_options.useNumProteinsColumn,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	64 useUniquePeptide = $input.input_options.useUniquePeptide,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	65 rmPSM_withMissing_withinRun = $input.input_options.rmPSM_withMissing_withinRun,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	66 rmPSM_withfewMea_withinRun = $input.input_options.rmPSM_withfewMea_withinRun,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	67 rmProtein_with1Feature = $input.input_options.rmProtein_with1Feature,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	68 summaryforMultipleRows = $input.input_options.summaryforMultipleRows)
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	69
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	70 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	71
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	72 quant <- proteinSummarization(input,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	73 method = "$proteinSummarization.method",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	74 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	75 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	76 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	77 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	78 MBimpute = $proteinSummarization.MBimpute,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	79 #if $proteinSummarization.maxQuantileforCensored == ''
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	80 maxQuantileforCensored = NULL)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	81 #else
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	82 maxQuantileforCensored = $proteinSummarization.maxQuantileforCensored)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	83 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	84
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	85 #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	86 #if $plot_type[-4:] == "Plot"
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	87 dataProcessPlotsTMT(input,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	88 quant,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	89 type = '$plot_type',
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	90 ylimUp = $out_plots_opt.adv.ylimUp,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	91 ylimDown = $out_plots_opt.adv.ylimDown,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	92 x.axis.size = $out_plots_opt.adv.x_axis_size,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	93 y.axis.size = $out_plots_opt.adv.y_axis_size,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	94 text.size = $out_plots_opt.adv.text_size,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	95 text.angle = $out_plots_opt.adv.text_angle,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	96 legend.size = $out_plots_opt.adv.legend_size,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	97 dot.size.profile = $out_plots_opt.adv.dot_size_profile,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	98 ncol.guide = $out_plots_opt.adv.ncol_guide,
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	99 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	100 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	101 #if $out_plots_opt.which_Protein.select != 'list'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	102 which.Protein = "$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	103 #else
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	104 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	105 #end if
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	106 originalPlot = $out_plots_opt.adv.originalPlot,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	107 summaryPlot = $out_plots_opt.adv.summaryPlot)
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	108 #elif $plot_type == "quant"
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	109 write.table(quant,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	110 "Quant.tsv",
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	111 sep = "\t",
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	112 quote = F,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	113 row.names = F,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	114 dec = ".")
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	115 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	116 #end for
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	117
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	118 #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	119 #if $group.use_comp_matrix.select == 'true'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	120 comp_matrix <- read.table("$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	121
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	122 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	123 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	124 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	125 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	126
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	127 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	128 #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	129 contrast.matrix = comparison,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	130 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	131 moderated = $group.moderated,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	132 adj.method = "$group.adj_method",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	133 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	134 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	135
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	136 write.table(comparisons,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	137 "ComparisonResult.tsv",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	138 sep = "\t",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	139 quote = F,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	140 row.names = F,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	141 dec = ".")
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	142
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	143 #for $plot_type in $group.selected_group_outputs
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	144 #if $plot_type == "VolcanoPlot" or $plot_type == "Heatmap" or $plot_type == "ComparisonPlot"
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	145 groupComparisonPlots(data = comparisons,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	146 type = "$plot_type",
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	147 sig = $group.comparison_plots_opt.sig,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	148 #if $group.comparison_plots_opt.FCcutoff:
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	149 FCcutoff = $group.comparison_plots_opt.FCcutoff,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	150 #end if
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	151 logBase.pvalue = $group.comparison_plots_opt.logBase_pvalue,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	152 #if $group.comparison_plots_opt.ylimUp:
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	153 ylimUp = $group.comparison_plots_opt.ylimUp,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	154 #end if
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	155 #if $group.comparison_plots_opt.ylimDown:
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	156 ylimDown = $group.comparison_plots_opt.ylimDown,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	157 #end if
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	158 x.axis.size = $group.comparison_plots_opt.x_axis_size,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	159 y.axis.size = $group.comparison_plots_opt.y_axis_size,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	160 dot.size = $group.comparison_plots_opt.dot_size,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	161 text.size = $group.comparison_plots_opt.text_size,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	162 text.angle = $group.comparison_plots_opt.text_angle,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	163 legend.size = $group.comparison_plots_opt.legend_size,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	164 ProteinName = $group.comparison_plots_opt.ProteinName,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	165 colorkey = $group.comparison_plots_opt.colorkey,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	166 numProtein = $group.comparison_plots_opt.numProtein,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	167 clustering = "$group.comparison_plots_opt.clustering",
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	168 width = $group.comparison_plots_opt.width,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	169 height = $group.comparison_plots_opt.height,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	170 #if $group.comparison_plots_opt.which_Protein.select != 'list'
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	171 which.Protein = "$group.comparison_plots_opt.which_Protein.select",
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	172 #else
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	173 which.Protein = unlist(read.table("$group.comparison_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE),
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	174 #end if
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	175 #if $group.comparison_plots_opt.which_Comparison.select != 'list'
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	176 which.Comparison = "$group.comparison_plots_opt.which_Comparison.select",
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	177 #else
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	178 which.Comparison = unlist(read.table("$group.comparison_plots_opt.which_Comparison.comparison_list", sep = "\n", header = FALSE), use.names = FALSE),
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	179 #end if
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	180 address="MSstats_group_")
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	181 #end if
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	182 #end for
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	183 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	184 ]]></configfile>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	185 </configfiles>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	186 <inputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	187 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	188 <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	189 <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	190 <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	191 <option value="OpenMS">OpenMS</option>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	192 <option value="PD">Proteome Discoverer</option>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	193 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	194 <when value="MSstatsTMT">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	195 <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	196 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	197 <when value="MaxQuant">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	198 <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	199 <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	200 <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	201 <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	202 <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	203 <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	204 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	205 <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	206 <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	207 <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	208 <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	209 <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	210 <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	211 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	212 </section>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	213 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	214 <when value="OpenMS">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	215 <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	216 <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	217 <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	218 <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	219 <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	220 <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	221 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	222 </section>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	223 </when>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	224 <when value="PD">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	225 <param name="PSM" type="data" format="tabular" label="PSM output" help=""/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	226 <param name="annotation" type="data" format="tabular" label="annotation" help="Data frame contains column Run, Fraction, TechRepMixture, Mixture, Channel, BioReplicate, Condition." />
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	227 <param name="proteinID" type="select" label="Select Protein ID">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	228 <option value="Protein.Accessions">Protein.Accessions column</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	229 <option value="Master.Protein.Accessions">Master.Protein.Accessions</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	230 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	231 <section name="input_options" title="PDtoMSstatsTMTFormat Options" expanded="false">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	232 <param name="useNumProteinsColumn" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove shared peptides by information of # Proteins column in PSM sheet." help="" />
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	233 <expand macro="input_options_shared"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	234 <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.">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	235 <option value="max">max</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	236 <option value="sum" selected="true">sum</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	237 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	238 </section>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	239 </when>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	240 </conditional>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	241 <section name="proteinSummarization" title="Summarize peptides into proteins" expanded="false">
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	242 <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	243 <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	244 <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	245 <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	246 <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	247 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	248 <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	249 <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	250 <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	251 <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	252 <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	253 <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	254 </section>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	255 <section name="out_plots_opt" title="Plot Output Options" expanded="false">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	256 <conditional name="which_Protein">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	257 <param name="select" type="select" label="Select protein IDs to draw plots">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	258 <option value="all" selected="true">generate all plots for each protein</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	259 <option value="allonly">Option for QC plot: "allonly" will generate one QC plot with all proteins</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	260 <option value="list">Protein IDs as tabular input</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	261 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	262 <when value="all"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	263 <when value="allonly"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	264 <when value="list">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	265 <param name="protein_list" type="data" format="tabular" label="List of proteins"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	266 </when>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	267 </conditional>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	268 <param name="width" type="integer" min="1" value="10" label="Width of the saved pdf file"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	269 <param name="height" type="integer" min="1" value="10" label="Height of the saved pdf file"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	270 <section name="adv" title="Advanced options" expanded="false">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	271 <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."/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	272 <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."/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	273 <param name="x_axis_size" type="integer" min="1" value="10" label="Size of x-axis labeling"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	274 <param name="y_axis_size" type="integer" min="1" value="10" label="Size of y-axis labeling"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	275 <param name="text_size" type="integer" min="1" value="4" label="Size of labels represented each condition at the top"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	276 <param name="text_angle" type="integer" min="0" max="360" value="90" label="Angle of labels represented each condition at the top"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	277 <param name="legend_size" type="integer" min="1" value="7" label="Size of legend above Profile plot"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	278 <param name="dot_size_profile" type="integer" min="1" value="2" label="Size of dots in Profile plot"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	279 <param name="ncol_guide" type="integer" min="1" value="5" label="Number of columns for legends at the top of plot"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	280 <param name="originalPlot" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Draw original profile plots without normalization"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	281 <param name="summaryPlot" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Draw profile plots with protein summarization for each channel and MS run"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	282 </section>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	283 </section>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	284 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	285 <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	286 <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	287 <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	288 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	289 <when value="false"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	290 <when value="true">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	291 <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	292 <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	293 <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	294 <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	295 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	296 <when value="false"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	297 <when value="true">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	298 <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	299 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	300 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	312 <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	313 <param name="remove_empty_channel" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove ’Empty’ channels from protein level data"/>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	314 <param name="selected_group_outputs" type="select" multiple="true" label="Select outputs">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	315 <help>Heatmap requires more than one comparison</help>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	316 <option value="comparison_result" selected="true">Group Comparison</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	317 <option value="VolcanoPlot" selected="true">MSstats Volcano Plot</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	318 <option value="Heatmap" selected="false">MSstats Heatmap</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	319 <option value="ComparisonPlot" selected="true">MSstats Comparison Plot</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	320 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	321 <section name="comparison_plots_opt" title="Comparison Plot Options" expanded="false">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	322 <param name="sig" type="float" min="0" max="1" value="0.05" label="FDR cutoff for the adjusted p-values in heatmap and volcano plot" help="Level of significance for comparison plot. 100(1-sig)% confidence interval will be drawn."/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	323 <param name="FCcutoff" type="float" optional="true" label="Involve fold change cutoff or not for volcano plot or heatmap." help="Empty (default) means no fold change cutoff is applied for significance analysis. Specific value means specific fold change cutoff is applied"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	324 <param name="logBase_pvalue" type="select" label="For volcano plot or heatmap, logarithm transformation of adjusted p-valuewith base 2 or 10">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	325 <option value="2">2</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	326 <option value="10" selected="true">10</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	327 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	328 <param name="ylimUp" type="float" optional="true" label="For all three plots, upper limit for y-axis." help="Empty (default) for volcano plot/heatmap use maximum of -log2 (adjusted p-value) or -log10 (adjusted p-value), for comparison plot uses maximum of log-fold change + CI. Alternatively, insert specific value of y-axis limit. "/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	329 <param name="ylimDown" type="float" optional="true" label="For all tree plots, lower limit for y-axis in the log scale" help="Empty (default) for volcano plot/heatmap use minimum of -log2 (adjusted p-value) or -log10 (adjusted p-value), for comparison plot uses minimum of log-fold change - CI. Alternatively, insert specific value of y-axis limit. "/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	330 <param name="xlimUp" type="float" optional="true" label="For Volcano plot, the limit for x-axis" help="Empty (default) for use maximum for absolute value of log-fold change or 3 as default if maximum for absolute value of log-fold change is less than 3. Alternatively, insert specific value of y-axis limit."/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	331 <param name="axis_size" type="integer" min="1" value="10" label="Size of axes labels for Residual and QQ Plots"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	332 <param name="x_axis_size" type="integer" min="1" value="10" label="Size of x-axis labeling"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	333 <param name="y_axis_size" type="integer" min="1" value="10" label="Size of y-axis labeling"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	334 <param name="dot_size" type="integer" min="1" value="3" label="Size of dots in residual plots, QQPlots, volcano plot and comparison plot."/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	335 <param name="text_size" type="integer" min="1" value="4" label="Size of Protein Name label in the graph for Volcano Plot."/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	336 <param name="text_angle" type="integer" min="0" max="360" value="90" label="Angle of x-axis labels represented each comparison at the bottom of graph incomparison plot."/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	337 <param name="legend_size" type="integer" min="1" value="7" label="Size of legend for color at the bottom of volcano plot. "/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	338 <param name="ProteinName" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Display protein names in Volcano Plot." help="Yes (default) means protein names, which are significant, are displayed next to the points. No means no protein names are displayed."/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	339 <param name="colorkey" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Show colour key"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	340 <param name="numProtein" type="integer" min="1" value="100" max="180" label="Number of proteins which will be presented in each heatmap."/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	341 <param name="clustering" type="select" label="Determines how to order proteins and comparisons. Hierarchical cluster analysis with Ward method(minimum variance) is performed.">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	342 <help>’protein’ means that protein dendrogram is computed and reordered based on protein means (the order of row is changed). ’comparison’ means comparison dendrogram is computed and reordered based on comparison means (the order of comparison is changed). ’both’ means to reorder both protein and comparison.</help>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	343 <option value="protein" selected="true">protein</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	344 <option value="comparison">comparison</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	345 <option value="both">both</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	346 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	347 <param name="width" type="integer" min="1" value="8" label="Width of the saved pdf file"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	348 <param name="height" type="integer" min="1" value="5" label="Height of the saved pdf file"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	349 <conditional name="which_Protein">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	350 <param name="select" type="select" label="Select protein IDs to draw plots">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	351 <option value="all" selected="true">generate all plots for each protein</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	352 <option value="list">Protein IDs as tabular input</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	353 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	354 <when value="all"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	355 <when value="list">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	356 <param name="protein_list" type="data" format="tabular" label="List of proteins"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	357 </when>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	358 </conditional>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	359 <conditional name="which_Comparison">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	360 <param name="select" type="select" label="Select comparisons to draw plots">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	361 <option value="all" selected="true">Generate all plots for each comparison</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	362 <option value="list">Comparison names as tabular input</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	363 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	364 <when value="all"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	365 <when value="list">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	366 <param name="comparison_list" type="data" format="tabular" label="List of comparisons"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	367 </when>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	368 </conditional>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	369 </section>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	370 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	371 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	372 <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	373 <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	374 <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	375 <option value="r_script" selected="false">MSstats Rscript</option>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	376 <option value="quant" selected="true">Protein abundance</option>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	377 <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	378 <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	379 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	380 </inputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	381 <outputs>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	382 <data name="out_msstats_log" from_work_dir="msstats.log" format="txt" label="${tool.name} on ${on_string}: MSstats log">
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	383 <filter>'msstats_log' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	384 </data>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	385 <data name="out_msstatstmt_log" from_work_dir="msstatstmt.log" format="txt" label="${tool.name} on ${on_string}: MSstatsTMT log">
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	386 <filter>'msstatstmt_log' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	387 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	388 <data name="out_r_script" format="txt" label="${tool.name} on ${on_string}: Rscript">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	389 <filter>'r_script' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	390 </data>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	391 <data name="out_quant" from_work_dir="Quant.tsv" format="tabular" label="${tool.name} on ${on_string}: Protein abundance">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	392 <filter>'quant' in selected_outputs</filter>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	393 </data>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	394 <data name="out_profile_plot" from_work_dir="ProfilePlot.pdf" format="pdf" label="${tool.name} on ${on_string}: Profile Plot">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	395 <filter>'ProfilePlot' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	396 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	397 <data name="out_qc_plot" from_work_dir="QCPlot.pdf" format="pdf" label="${tool.name} on ${on_string}: QC Plot">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	398 <filter>'QCPlot' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	399 </data>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	400 <data name="out_group_comp" from_work_dir="ComparisonResult.tsv" format="tabular" label="${tool.name} on ${on_string}: Group Comparison">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	401 <filter>group['group_comparison'] == 'true' and 'comparison_result' in group['selected_group_outputs']</filter>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	402 </data>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	403 <data name="out_group_volcano_plot" from_work_dir="MSstats_group_VolcanoPlot.pdf" format="pdf" label="${tool.name} on ${on_string}: Group Comparison - Volcano Plot">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	404 <filter>group['group_comparison'] == 'true' and 'VolcanoPlot' in group['selected_group_outputs']</filter>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	405 </data>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	406 <data name="out_group_heatmap" from_work_dir="MSstats_group_Heatmap.pdf" format="pdf" label="${tool.name} on ${on_string}: Group Comparison - Heatmap">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	407 <filter>group['group_comparison'] == 'true' and 'Heatmap' in group['selected_group_outputs']</filter>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	408 </data>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	409 <data name="out_group_comp_plot" from_work_dir="MSstats_group_ComparisonPlot.pdf" format="pdf" label="${tool.name} on ${on_string}: Group Comparison - Comparison Plot">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	410 <filter>group['group_comparison'] == 'true' and 'ComparisonPlot' in group['selected_group_outputs']</filter>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	411 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	412 </outputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	413 <tests>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	414 <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	415 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	416 <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	417 <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	418 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	419 <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	420 <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	421 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	422 <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	423 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	424 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	425 <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	426 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	427 <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	428 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	429 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	430 <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	431 <assert_contents>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	432 <has_n_lines n="52" />
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	433 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	434 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	435 <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	436 <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	437 </test>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	438 <test expect_num_outputs="4">
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	439 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	440 <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	441 <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	442 <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	443 <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	444 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	445 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	446 <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	447 <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	448 <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	449 <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	450 </conditional>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	451 <param name="selected_group_outputs" value="comparison_result,VolcanoPlot,ComparisonPlot"/>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	452 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	453 <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	454 <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	455 <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	456 <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	457 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	458 <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	459 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	460 <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	461 <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	462 <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	463 <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	464 <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	465 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	466 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	467 <output name="out_profile_plot" file="ProfilePlot_list.pdf" compare="sim_size"/>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	468 <output name="out_group_volcano_plot" file="MSstats_group_VolcanoPlot.pdf" compare="sim_size"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	469 <output name="out_group_comp_plot" file="MSstats_group_ComparisonPlot.pdf" compare="sim_size"/>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	470 </test>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	471 <test expect_num_outputs="3">
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	472 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	473 <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	474 <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	475 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	476 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	477 <param name="group_comparison" value="true"/>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	478 <param name="selected_group_outputs" value="comparison_result,Heatmap"/>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	479 </conditional>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	480 <param name="selected_outputs" value="r_script"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	481 <output name="out_r_script">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	482 <assert_contents>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	483 <has_n_lines n="58" />
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	484 </assert_contents>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	485 </output>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	486 <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	487 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	488 <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	489 <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	490 <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	491 <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	492 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	493 </output>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	494 <output name="out_group_heatmap" file="MSstats_group_Heatmap.pdf" compare="sim_size"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	495 </test>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	496 <test expect_num_outputs="1">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	497 <conditional name="input">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	498 <param name="input_src" value="PD"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	499 <param name="PSM" ftype="tabular" value="input.pd.txt"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	500 <param name="annotation" ftype="tabular" value="annotation.pd.txt"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	501 </conditional>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	502 <param name="selected_outputs" value="quant"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	503 <output name="out_quant">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	504 <assert_contents>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	505 <has_n_lines n="1575" />
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	506 <has_n_columns n="8" />
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	507 <has_text text="PAMI-176_Mouse_A-J_1" />
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	508 <has_text text="Long_LF" />
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	509 </assert_contents>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	510 </output>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	511 </test>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	512 </tests>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	513 <help><![CDATA[
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	514 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	515
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	516 Notes
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	517
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	518 - 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	519
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	520 ::
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	521
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	522 #> ProteinName PeptideSequence
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	523 #> 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	524 #> 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	525 #> 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	526 #> 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	527 #> 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	528 #> 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	529 #> PrecursorCharge PSM Mixture
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	530 #> 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	531 #> 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	532 #> 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	533 #> 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	534 #> 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	535 #> 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	536 #> 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	537 #> 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	538 #> 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	539 #> 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	540 #> 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	541 #> 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	542 #> 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	543
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	544 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	545
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	546 - 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	547
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	548 - 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	549 - 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	550 - 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	551 - 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	552 - 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	553
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	554 ::
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	555
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	556 names groupA groupB
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	557 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	558
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	559
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	560 - 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	561
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	562 ::
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	563
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	564 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	565 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	566 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	567 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	568 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	569
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	570 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	571 ]]>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	572 </help>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	573 <citations>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	574 <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	575 </citations>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	576 </tool>

Mercurial > repos > galaxyp > msstatstmt

annotate msstatstmt.xml @ 2:782bd55b000b draft