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
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fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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1 <tool id="msstatstmt" name="MSstatsTMT" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</description>
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3 <macros>
4
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4 <token name="@TOOL_VERSION@">2.0.0</token>
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5 <token name="@GALAXY_VERSION@">0</token>
0
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6 <xml name="input_options_shared">
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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." />
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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." />
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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." />
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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"
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11 </xml>
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12 </macros>
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13 <requirements>
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14 <requirement type="package" version="@TOOL_VERSION@">bioconductor-msstatstmt</requirement>
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15 </requirements>
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16 <command detect_errors="exit_code"><![CDATA[
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17 cat '$msstatstmt_script' > '$out_r_script' &&
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18 Rscript '$msstatstmt_script'
4
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19
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20 && cat MSstatsTMT_summarization_log*.log > '$out_msstatstmt_sum_log'
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21 && cat MSstatsTMT_summarization_MSstats*.log > '$out_msstatstmt_sum_ms'
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22
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23 #if $input.input_src != 'MSstatsTMT':
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24 && cat MSstatsTMT_converter_log*.log > '$out_msstatstmt_conv_log'
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25 #else:
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26 && echo "MSstatsTMT input. No conversion needed." > '$out_msstatstmt_conv_log'
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27 #end if
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28
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639"
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29 #if $group.group_comparison == 'true':
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30 && cat MSstatsTMT_log_groupComparison*.log > '$out_msstatstmt_group_log'
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31 && cat MSstats_log*.log > '$out_msstats_gc_log'
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32 #else:
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33 && echo "No groupComparison was performed." > '$out_msstatstmt_group_log'
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34 && echo "No groupComparison was performed." > '$out_msstats_gc_log'
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35 #end if
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36
0
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37 ]]></command>
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38 <configfiles>
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39 <configfile name="msstatstmt_script"><![CDATA[
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40 library(MSstatsTMT, warn.conflicts = F, quietly = T, verbose = F)
2
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41 library(MSstats)
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42
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43 #if $input.input_src == 'MSstatsTMT'
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44 input <- read.table("$input.msstatstmt_input", sep="\t", header=TRUE)
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45
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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46 #elif $input.input_src == 'MaxQuant'
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47 proteinGroups.mq <- read.table("$input.proteinGroups", sep="\t", header=TRUE)
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48 evidence.mq <- read.table("$input.evidence", sep="\t", header=TRUE)
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49 annotation.mq <- read.table("$input.annotation", sep="\t", header=TRUE)
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50
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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51 input <- MaxQtoMSstatsTMTFormat(evidence = evidence.mq,
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52 proteinGroups = proteinGroups.mq,
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53 annotation = annotation.mq,
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54 which.proteinid = "$input.proteinID",
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55 rmProt_Only.identified.by.site = $input.input_options.rmProt_Onlyidentifiedbysite,
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56 useUniquePeptide = $input.input_options.useUniquePeptide,
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57 rmPSM_withMissing_withinRun = $input.input_options.rmPSM_withMissing_withinRun,
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58 rmPSM_withfewMea_withinRun = $input.input_options.rmPSM_withfewMea_withinRun,
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59 rmProtein_with1Feature = $input.input_options.rmProtein_with1Feature,
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60 summaryforMultipleRows = $input.input_options.summaryforMultipleRows)
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61
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62 #elif $input.input_src == 'OpenMS'
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63 input.oms <- read.table("$input.oms_input", sep="\t", header=TRUE)
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64
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65 input <- OpenMStoMSstatsTMTFormat(input.oms,
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66 useUniquePeptide = $input.input_options.useUniquePeptide,
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67 rmPSM_withMissing_withinRun = $input.input_options.rmPSM_withMissing_withinRun,
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68 rmPSM_withfewMea_withinRun = $input.input_options.rmPSM_withfewMea_withinRun,
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69 rmProtein_with1Feature = $input.input_options.rmProtein_with1Feature,
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70 summaryforMultiplePSMs = $input.input_options.summaryforMultiplePSMs)
2
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71
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72 #elif $input.input_src == 'PD'
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73 PSM.pd <- read.table("$input.PSM", sep="\t", header=TRUE)
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74 annotation.pd <- read.table("$input.annotation", sep="\t", header=TRUE)
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75
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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76 input <- PDtoMSstatsTMTFormat(PSM.pd,
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77 annotation = annotation.pd,
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78 which.proteinid = "$input.proteinID",
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79 useNumProteinsColumn = $input.input_options.useNumProteinsColumn,
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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 $plot_type[-4:] == "Plot"
4
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galaxyp
parents: 3
diff changeset
103 dataProcessPlotsTMT(quant,
0
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
104 type = '$plot_type',
2
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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
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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
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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",
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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 $plot_type == "ComparisonPlot"
4
8375a0035d79 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639"
galaxyp
parents: 3
diff changeset
164
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165 ## Workaround for missing option "MSstatsLog" (getOption("MSstatsLog") returns NULL)
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166 MSstatsConvert::MSstatsLogsSettings()
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167 #############################################
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168
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169 groupComparisonPlots(data = comparisons\$ComparisonResult,
2
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170 type = "$plot_type",
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171 sig = $group.comparison_plots_opt.sig,
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172 #if $group.comparison_plots_opt.FCcutoff:
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173 FCcutoff = $group.comparison_plots_opt.FCcutoff,
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174 #end if
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175 logBase.pvalue = $group.comparison_plots_opt.logBase_pvalue,
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176 #if $group.comparison_plots_opt.ylimUp:
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177 ylimUp = $group.comparison_plots_opt.ylimUp,
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178 #end if
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179 #if $group.comparison_plots_opt.ylimDown:
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180 ylimDown = $group.comparison_plots_opt.ylimDown,
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181 #end if
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182 x.axis.size = $group.comparison_plots_opt.x_axis_size,
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183 y.axis.size = $group.comparison_plots_opt.y_axis_size,
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184 dot.size = $group.comparison_plots_opt.dot_size,
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185 text.size = $group.comparison_plots_opt.text_size,
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186 text.angle = $group.comparison_plots_opt.text_angle,
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187 legend.size = $group.comparison_plots_opt.legend_size,
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188 ProteinName = $group.comparison_plots_opt.ProteinName,
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189 colorkey = $group.comparison_plots_opt.colorkey,
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190 numProtein = $group.comparison_plots_opt.numProtein,
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191 clustering = "$group.comparison_plots_opt.clustering",
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192 width = $group.comparison_plots_opt.width,
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193 height = $group.comparison_plots_opt.height,
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194 #if $group.comparison_plots_opt.which_Protein.select != 'list'
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195 which.Protein = "$group.comparison_plots_opt.which_Protein.select",
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196 #else
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197 which.Protein = unlist(read.table("$group.comparison_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE),
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198 #end if
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199 #if $group.comparison_plots_opt.which_Comparison.select != 'list'
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200 which.Comparison = "$group.comparison_plots_opt.which_Comparison.select",
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201 #else
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202 which.Comparison = unlist(read.table("$group.comparison_plots_opt.which_Comparison.comparison_list", sep = "\n", header = FALSE), use.names = FALSE),
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203 #end if
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204 address="MSstats_group_")
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205 #end if
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206 #end for
0
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207 #end if
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208 ]]></configfile>
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209 </configfiles>
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210 <inputs>
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211 <conditional name="input">
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212 <param name="input_src" type="select" label="Input Source">
3
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213 <option value="MSstatsTMT">MSstatsTMT (11 column format)</option>
0
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214 <option value="MaxQuant">MaxQuant</option>
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215 <option value="OpenMS">OpenMS</option>
2
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216 <option value="PD">Proteome Discoverer</option>
0
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217 </param>
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218 <when value="MSstatsTMT">
3
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219 <param name="msstatstmt_input" type="data" format="tabular" label="MSstatsTMT (11 column format)"/>
0
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220 </when>
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221 <when value="MaxQuant">
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222 <param name="evidence" type="data" format="tabular" label="evidence.txt - feature-level data"/>
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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
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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
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225 <param name="proteinID" type="select" label="Select Protein ID in evidence.txt">
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226 <option value="Proteins">Protein column</option>
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227 <option value="Leading.razor.protein">Leading razor protein column</option>
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228 </param>
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229 <section name="input_options" title="MaxQtoMSstatsTMTFormat Options" expanded="false">
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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." />
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231 <expand macro="input_options_shared"/>
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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.">
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233 <option value="max">max</option>
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234 <option value="sum" selected="true">sum</option>
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235 </param>
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236 </section>
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237 </when>
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238 <when value="OpenMS">
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239 <param name="oms_input" type="data" format="tabular" label="OpenMS input"/>
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240 <section name="input_options" title="OpenMStoMSstatsTMTFormat Options" expanded="false">
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241 <expand macro="input_options_shared"/>
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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.">
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243 <option value="max">max</option>
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244 <option value="sum" selected="true">sum</option>
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245 </param>
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246 </section>
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247 </when>
2
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248 <when value="PD">
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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"
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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"
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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"
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252 <option value="Protein.Accessions">Protein.Accessions column</option>
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253 <option value="Master.Protein.Accessions">Master.Protein.Accessions</option>
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254 </param>
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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"
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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"
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257 <expand macro="input_options_shared"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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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.">
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259 <option value="max">max</option>
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260 <option value="sum" selected="true">sum</option>
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261 </param>
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262 </section>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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263 </when>
0
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264 </conditional>
2
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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"
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266 <param name="method" type="select" multiple="false" label="Select method">
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267 <option value="msstats" selected="true">msstats</option>
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268 <option value="MedianPolish">MedianPolish</option>
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269 <option value="Median">Median</option>
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270 <option value="LogSum">LogSum</option>
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271 </param>
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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"
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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"
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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"
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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"
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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"
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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"
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278 </section>
2
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279 <section name="out_plots_opt" title="Plot Output Options" expanded="false">
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280 <conditional name="which_Protein">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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281 <param name="select" type="select" label="Select protein IDs to draw plots">
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282 <option value="all" selected="true">generate all plots for each protein</option>
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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"
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284 <option value="list">Protein IDs as tabular input</option>
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285 </param>
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286 <when value="all"/>
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287 <when value="allonly"/>
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288 <when value="list">
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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"
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290 </when>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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291 </conditional>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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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"
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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"
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294 <section name="adv" title="Advanced options" expanded="false">
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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"
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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"
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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"
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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"
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299 <param name="text_size" type="integer" min="1" value="4" label="Size of labels represented each condition at the top"/>
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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"
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301 <param name="legend_size" type="integer" min="1" value="7" label="Size of legend above Profile plot"/>
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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"
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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"
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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"
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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"
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306 </section>
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307 </section>
0
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308 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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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"
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310 <option value="false">No</option>
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311 <option value="true">Yes</option>
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312 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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313 <when value="false"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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314 <when value="true">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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315 <conditional name="use_comp_matrix">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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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"
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317 <option value="false">No</option>
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318 <option value="true">Yes</option>
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319 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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320 <when value="false"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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321 <when value="true">
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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"
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323 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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324 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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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
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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
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327 <option value="holm">holm</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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328 <option value="hochberg">hochberg</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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329 <option value="hommel">hommel</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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330 <option value="bonferroni">bonferroni</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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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"
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332 <option value="BY">BY</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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333 <option value="fdr">fdr</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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334 <option value="none">none</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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335 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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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"
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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"
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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"
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339 <help>Heatmap requires more than one comparison</help>
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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"
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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"
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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"
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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"
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344 </param>
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345 <section name="comparison_plots_opt" title="Comparison Plot Options" expanded="false">
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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"
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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"
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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"
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349 <option value="2">2</option>
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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"
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351 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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368 <option value="comparison">comparison</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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369 <option value="both">both</option>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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370 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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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"
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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"
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373 <conditional name="which_Protein">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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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"
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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"
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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"
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377 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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378 <when value="all"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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379 <when value="list">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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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"
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381 </when>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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382 </conditional>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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383 <conditional name="which_Comparison">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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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"
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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"
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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"
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387 </param>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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388 <when value="all"/>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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389 <when value="list">
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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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"
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391 </when>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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392 </conditional>
782bd55b000b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
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393 </section>
0
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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394 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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395 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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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>