msstatstmt: msstatstmt.xml annotate

annotate msstatstmt.xml @ 5:a5e394b36d87 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 909dc08cad859acb747324c8c867770022a2a455"

author	galaxyp
date	Wed, 11 Aug 2021 11:11:22 +0000
parents	8375a0035d79
children	bd1535813cfe

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>
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	4 <token name="@TOOL_VERSION@">2.0.0</token>
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	5 <token name="@GALAXY_VERSION@">0</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 '$msstatstmt_script'
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	19
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	20 && cat MSstatsTMT_summarization_log*.log > '$out_msstatstmt_sum_log'
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	21 && cat MSstatsTMT_summarization_MSstats*.log > '$out_msstatstmt_sum_ms'
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	22
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	23 #if $input.input_src != 'MSstatsTMT':
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	24 && cat MSstatsTMT_converter_log*.log > '$out_msstatstmt_conv_log'
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	25 #else:
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	26 && echo "MSstatsTMT input. No conversion needed." > '$out_msstatstmt_conv_log'
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	27 #end if
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	28
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	29 #if $group.group_comparison == 'true':
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	30 && cat MSstatsTMT_log_groupComparison*.log > '$out_msstatstmt_group_log'
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	31 && cat MSstats_log*.log > '$out_msstats_gc_log'
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	32 #else:
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	33 && echo "No groupComparison was performed." > '$out_msstatstmt_group_log'
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	34 && echo "No groupComparison was performed." > '$out_msstats_gc_log'
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	35 #end if
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	36
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	37 ]]></command>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	38 <configfiles>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	39 <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	40 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	41 library(MSstats)
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	42
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	43 #if $input.input_src == 'MSstatsTMT'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	44 input <- read.table("$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	45
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	46 #elif $input.input_src == 'MaxQuant'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	47 proteinGroups.mq <- read.table("$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	48 evidence.mq <- read.table("$input.evidence", sep="\t", header=TRUE)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	49 annotation.mq <- read.table("$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	50
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	51 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	52 proteinGroups = proteinGroups.mq,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	53 annotation = annotation.mq,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	54 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	55 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	56 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	57 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	58 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	59 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	60 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	61
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	62 #elif $input.input_src == 'OpenMS'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	63 input.oms <- read.table("$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	64
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	65 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	66 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	67 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	68 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	69 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	70 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	71
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	72 #elif $input.input_src == 'PD'
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	73 PSM.pd <- read.table("$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	74 annotation.pd <- read.table("$input.annotation", sep="\t", header=TRUE)
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	75
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	76 input <- PDtoMSstatsTMTFormat(PSM.pd,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	77 annotation = annotation.pd,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	78 which.proteinid = "$input.proteinID",
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	79 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	80 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	81 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	82 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	83 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	84 summaryforMultipleRows = $input.input_options.summaryforMultipleRows)
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	85
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	86 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	87
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	88 quant <- proteinSummarization(input,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	89 method = "$proteinSummarization.method",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	90 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	91 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	92 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	93 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	94 MBimpute = $proteinSummarization.MBimpute,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	95 #if $proteinSummarization.maxQuantileforCensored == ''
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	96 maxQuantileforCensored = NULL)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	97 #else
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	98 maxQuantileforCensored = $proteinSummarization.maxQuantileforCensored)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	99 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	100
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	101 #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	102 #if $plot_type[-4:] == "Plot"
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	103 dataProcessPlotsTMT(quant,
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	104 type = '$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	105 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	106 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	107 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	108 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	109 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	110 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	111 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	112 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	113 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	114 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	115 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	116 #if $out_plots_opt.which_Protein.select != 'list'
3 5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	117 #if $out_plots_opt.which_Protein.select == "allonly" and $plot_type == "ProfilePlot"
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	118 which.Protein = "all",
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	119 #else
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	120 which.Protein = "$out_plots_opt.which_Protein.select",
3 5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	121 #end if
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	122 #else
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	123 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	124 #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	125 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	126 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	127 #elif $plot_type == "quant"
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	128 write.table(quant\$ProteinLevelData,
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	129 "Quant.tsv",
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	130 sep = "\t",
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	131 quote = F,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	132 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	133 dec = ".")
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	134 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	135 #end for
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	136
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	137 #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	138 #if $group.use_comp_matrix.select == 'true'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	139 comp_matrix <- read.table("$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	140
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	141 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	142 row.names(comparison) <- as.character(comp_matrix[,1])
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	143 comparison <- as.matrix(comparison[levels(quant\$ProteinLevelData\$Condition)])
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	144 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	145
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	146 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	147 #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	148 contrast.matrix = comparison,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	149 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	150 moderated = $group.moderated,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	151 adj.method = "$group.adj_method",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	152 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	153 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	154
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	155 write.table(comparisons\$ComparisonResult,
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	156 "ComparisonResult.tsv",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	157 sep = "\t",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	158 quote = F,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	159 row.names = F,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	160 dec = ".")
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	161
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	162 #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	163 #if $plot_type == "VolcanoPlot" or $plot_type == "Heatmap" or $plot_type == "ComparisonPlot"
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	164
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	165 ## Workaround for missing option "MSstatsLog" (getOption("MSstatsLog") returns NULL)
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	166 MSstatsConvert::MSstatsLogsSettings()
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	167 #############################################
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	168
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	169 groupComparisonPlots(data = comparisons\$ComparisonResult,
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	170 type = "$plot_type",
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	171 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	172 #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	173 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	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 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	176 #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	177 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	178 #end if
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	179 #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	180 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	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 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	183 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	184 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	185 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	186 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	187 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	188 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	189 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	190 numProtein = $group.comparison_plots_opt.numProtein,
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	191 clustering = "$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	192 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	193 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	194 #if $group.comparison_plots_opt.which_Protein.select != 'list'
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	195 which.Protein = "$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	196 #else
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	197 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	198 #end if
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	199 #if $group.comparison_plots_opt.which_Comparison.select != 'list'
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	200 which.Comparison = "$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	201 #else
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	202 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	203 #end if
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	204 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	205 #end if
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	206 #end for
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	207 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	208 ]]></configfile>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	209 </configfiles>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	210 <inputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	211 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	212 <param name="input_src" type="select" label="Input Source">
3 5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	213 <option value="MSstatsTMT">MSstatsTMT (11 column format)</option>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	214 <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	215 <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	216 <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	217 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	218 <when value="MSstatsTMT">
3 5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	219 <param name="msstatstmt_input" type="data" format="tabular" label="MSstatsTMT (11 column format)"/>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	220 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	221 <when value="MaxQuant">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	222 <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	223 <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	224 <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	225 <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	226 <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	227 <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	228 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	229 <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	230 <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	231 <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	232 <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	233 <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	234 <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	235 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	236 </section>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	237 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	238 <when value="OpenMS">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	239 <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	240 <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	241 <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	242 <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	243 <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	244 <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	245 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	246 </section>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	247 </when>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	248 <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	249 <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	250 <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	251 <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	252 <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	253 <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	254 </param>
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="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	256 <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	257 <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	258 <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	259 <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	260 <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	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 </section>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	263 </when>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	264 </conditional>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	265 <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	266 <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	267 <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	268 <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	269 <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	270 <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	271 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	272 <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	273 <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	274 <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	275 <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	276 <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	277 <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	278 </section>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	279 <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	280 <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	281 <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	282 <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	283 <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	284 <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	285 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	286 <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	287 <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	288 <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	289 <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	290 </when>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	291 </conditional>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	292 <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	293 <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	294 <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	295 <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	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 <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	305 <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	306 </section>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	307 </section>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	308 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	309 <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	310 <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	311 <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	312 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	313 <when value="false"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	314 <when value="true">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	315 <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	316 <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	317 <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	318 <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	319 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	320 <when value="false"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	321 <when value="true">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	322 <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	323 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	324 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <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	333 <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	334 <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	335 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	336 <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	337 <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	338 <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	339 <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	340 <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	341 <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	342 <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	343 <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	344 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	345 <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	346 <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	347 <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	348 <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	349 <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	350 <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	351 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	352 <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	353 <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	354 <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	355 <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	356 <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	357 <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	358 <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	359 <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	360 <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	361 <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	362 <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	363 <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	364 <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	365 <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	366 <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	367 <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	368 <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	369 <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	370 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	371 <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	372 <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	373 <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	374 <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	375 <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	376 <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	377 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	378 <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	379 <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	380 <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	381 </when>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	382 </conditional>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	383 <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	384 <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	385 <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	386 <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	387 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	388 <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	389 <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	390 <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	391 </when>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	392 </conditional>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	393 </section>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	394 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	395 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	396 <param name="selected_outputs" type="select" multiple="true" optional="false" label="Select Outputs">
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	397 <option value="msstatstmt_conv_log" selected="false">MSstatsTMT converter log</option>
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	398 <option value="msstatstmt_sum_log" selected="true">MSstatsTMT summarization log</option>
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	399 <option value="msstatstmt_sum_ms" selected="true">MSstatsTMT summarization MSstats</option>
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	400 <option value="msstatstmt_group_log" selected="false">MSstatsTMT groupComparison log</option>
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	401 <option value="msstats_gc_log" selected="false">MSstats log (groupComparison)</option>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	402 <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	403 <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	404 <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	405 <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	406 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	407 </inputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	408 <outputs>
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	409 <data name="out_msstatstmt_conv_log" from_work_dir="MSstatsTMT_converter_log.log" format="txt" label="${tool.name} on ${on_string}: MSstatsTMT converter log">
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	410 <filter>'msstatstmt_conv_log' in selected_outputs</filter>
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	411 </data>
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	412 <data name="out_msstatstmt_sum_log" from_work_dir="MSstatsTMT_summarization_log.log" format="txt" label="${tool.name} on ${on_string}: MSstatsTMT summarization log">
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	413 <filter>'msstatstmt_sum_log' in selected_outputs</filter>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	414 </data>
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	415 <data name="out_msstatstmt_sum_ms" from_work_dir="MSstatsTMT_summarization_MSstats.log" format="txt" label="${tool.name} on ${on_string}: MSstatsTMT summarization MSstats">
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	416 <filter>'msstatstmt_sum_ms' in selected_outputs</filter>
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	417 </data>
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	418 <data name="out_msstatstmt_group_log" from_work_dir="MSstatsTMT_log_groupComparison.log" format="txt" label="${tool.name} on ${on_string}: MSstatsTMT groupComparison log">
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	419 <filter>'msstatstmt_group_log' in selected_outputs</filter>
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	420 </data>
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	421 <data name="out_msstats_gc_log" from_work_dir="MSstats_log.log" format="txt" label="${tool.name} on ${on_string}: MSstats log (groupComparison)">
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	422 <filter>'msstats_gc_log' in selected_outputs</filter>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	423 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	424 <data name="out_r_script" format="txt" label="${tool.name} on ${on_string}: Rscript">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	425 <filter>'r_script' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	426 </data>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	427 <data name="out_quant" from_work_dir="Quant.tsv" format="tabular" label="${tool.name} on ${on_string}: Protein abundance">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	428 <filter>'quant' in selected_outputs</filter>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	429 </data>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	430 <data name="out_profile_plot" from_work_dir="ProfilePlot.pdf" format="pdf" label="${tool.name} on ${on_string}: Profile Plot">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	431 <filter>'ProfilePlot' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	432 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	433 <data name="out_qc_plot" from_work_dir="QCPlot.pdf" format="pdf" label="${tool.name} on ${on_string}: QC Plot">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	434 <filter>'QCPlot' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	435 </data>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	436 <data name="out_group_comp" from_work_dir="ComparisonResult.tsv" format="tabular" label="${tool.name} on ${on_string}: Group Comparison">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	437 <filter>group['group_comparison'] == 'true' and 'comparison_result' in group['selected_group_outputs']</filter>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	438 </data>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	439 <data name="out_group_volcano_plot" from_work_dir="MSstats_group_VolcanoPlot.pdf" format="pdf" label="${tool.name} on ${on_string}: Group Comparison - Volcano Plot">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	440 <filter>group['group_comparison'] == 'true' and 'VolcanoPlot' in group['selected_group_outputs']</filter>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	441 </data>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	442 <data name="out_group_heatmap" from_work_dir="MSstats_group_Heatmap.pdf" format="pdf" label="${tool.name} on ${on_string}: Group Comparison - Heatmap">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	443 <filter>group['group_comparison'] == 'true' and 'Heatmap' in group['selected_group_outputs']</filter>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	444 </data>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	445 <data name="out_group_comp_plot" from_work_dir="MSstats_group_ComparisonPlot.pdf" format="pdf" label="${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	446 <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	447 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	448 </outputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	449 <tests>
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	450 <test expect_num_outputs="6">
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	451 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	452 <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	453 <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	454 </conditional>
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	455 <param name="selected_outputs" value="msstatstmt_conv_log,msstatstmt_sum_ms,msstatstmt_sum_log,r_script,ProfilePlot,QCPlot"/>
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	456 <output name="out_msstatstmt_sum_ms">
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	457 <assert_contents>
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	458 <has_text text="MSstats - dataProcess function" />
0 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 </output>
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	461 <output name="out_msstatstmt_sum_log">
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	462 <assert_contents>
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="MSstatsTMT - proteinSummarization function" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	464 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	465 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	466 <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	467 <assert_contents>
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	468 <has_n_lines n="50" />
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	469 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	470 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	471 <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	472 <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	473 </test>
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	474 <test expect_num_outputs="6">
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	475 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	476 <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	477 <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	478 <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	479 <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	480 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	481 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	482 <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	483 <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	484 <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	485 <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	486 </conditional>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	487 <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	488 </conditional>
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	489 <param name="selected_outputs" value="ProfilePlot,msstatstmt_group_log,msstats_gc_log"/>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	490 <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	491 <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	492 <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	493 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	494 <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	495 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	496 <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	497 <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	498 <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	499 <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	500 <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	501 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	502 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	503 <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	504 <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	505 <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	506 </test>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	507 <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	508 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	509 <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	510 <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	511 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	512 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	513 <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	514 <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	515 </conditional>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	516 <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	517 <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	518 <assert_contents>
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	519 <has_n_lines n="61" />
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	520 </assert_contents>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	521 </output>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	522 <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	523 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	524 <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	525 <has_n_columns n="8" />
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	526 <has_text text="Long_LF vs Short_HF" />
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	527 <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	528 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	529 </output>
2 782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	530 <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	531 </test>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	532 <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	533 <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	534 <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	535 <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	536 <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	537 </conditional>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	538 <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	539 <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	540 <assert_contents>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	541 <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	542 <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	543 <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	544 <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	545 </assert_contents>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f" galaxyp parents: 1 diff changeset	546 </output>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	547 </test>
3 5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	548 <test expect_num_outputs="1">
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	549 <conditional name="input">
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	550 <param name="input_src" value="MaxQuant"/>
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	551 <param name="evidence" ftype="tabular" value="evidence.txt"/>
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	552 <param name="annotation" ftype="tabular" value="annotation.txt"/>
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	553 <param name="proteinGroups" ftype="tabular" value="proteinGroups.txt"/>
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	554 </conditional>
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	555 <param name="selected_outputs" value="ProfilePlot"/>
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	556 <conditional name="which_Protein">
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	557 <param name="select" value="allonly"/>
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	558 </conditional>
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	559 <output name="out_profile_plot" file="ProfilePlot_allonly.pdf" compare="sim_size"/>
5667ff6f7a40 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" galaxyp parents: 2 diff changeset	560 </test>
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	561 </tests>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	562 <help><![CDATA[
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	563 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	564
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	565 Notes
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	566
5 a5e394b36d87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 909dc08cad859acb747324c8c867770022a2a455" galaxyp parents: 4 diff changeset	567 - MSstatsTMT 11 column format: For TMT datasets an additional 'Channel' column is required, which has to be in the format 'channel.X' with X being the channel number..
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	568
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
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	571 #> ProteinName PeptideSequence
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	572 #> 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	573 #> 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	574 #> 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	575 #> 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	576 #> 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	577 #> 6 sp\|Q60854\|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
4 8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" galaxyp parents: 3 diff changeset	578 #> Charge PSM Mixture
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	579 #> 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	580 #> 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	581 #> 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	582 #> 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	583 #> 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	584 #> 6 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
5 a5e394b36d87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 909dc08cad859acb747324c8c867770022a2a455" galaxyp parents: 4 diff changeset	585 #> TechRepMixture Run Channel BioReplicate Condition Intensity
a5e394b36d87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 909dc08cad859acb747324c8c867770022a2a455" galaxyp parents: 4 diff changeset	586 #> 1 3_3 3_3_3 channel.1 21 Long_HF NA
a5e394b36d87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 909dc08cad859acb747324c8c867770022a2a455" galaxyp parents: 4 diff changeset	587 #> 2 3_3 3_3_3 channel.2 22 Norm 1068.580
a5e394b36d87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 909dc08cad859acb747324c8c867770022a2a455" galaxyp parents: 4 diff changeset	588 #> 3 3_3 3_3_3 channel.3 23 Long_M 1508.330
a5e394b36d87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 909dc08cad859acb747324c8c867770022a2a455" galaxyp parents: 4 diff changeset	589 #> 4 3_3 3_3_3 channel.4 24 Long_HF NA
a5e394b36d87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 909dc08cad859acb747324c8c867770022a2a455" galaxyp parents: 4 diff changeset	590 #> 5 3_3 3_3_3 channel.5 25 Long_LF 1580.951
a5e394b36d87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 909dc08cad859acb747324c8c867770022a2a455" galaxyp parents: 4 diff changeset	591 #> 6 3_3 3_3_3 channel.6 26 Long_HF 1820.072
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	592
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	593 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	594
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	595 - 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	596
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	597 - 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	598 - 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	599 - 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	600 - 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	601 - 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	602
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	603 ::
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	604
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	605 names groupA groupB
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	606 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	607
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	608
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	609 - 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	610
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	611 ::
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	612
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	613 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	614 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	615 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	616 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	617 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	618
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	619 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	620 ]]>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	621 </help>
5 a5e394b36d87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 909dc08cad859acb747324c8c867770022a2a455" galaxyp parents: 4 diff changeset	622
0 fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	623 <citations>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	624 <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	625 </citations>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed" galaxyp parents: diff changeset	626 </tool>

Mercurial > repos > galaxyp > msstatstmt

annotate msstatstmt.xml @ 5:a5e394b36d87 draft