annotate msstatstmt.xml @ 1:b79d4c961009 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 5ac4f6093606746adb0d40fe4f73871f5934d091"
author galaxyp
date Fri, 05 Feb 2021 18:42:55 +0000
parents fd3dc69b78ff
children 782bd55b000b
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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>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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3 <macros>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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4 <token name="@TOOL_VERSION@">1.8.0</token>
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5 <token name="@GALAXY_VERSION@">0</token>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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6 <xml name="input_options_shared">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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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." />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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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." />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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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." />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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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>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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12 </macros>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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13 <requirements>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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14 <requirement type="package" version="@TOOL_VERSION@">bioconductor-msstatstmt</requirement>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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15 </requirements>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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16 <command detect_errors="exit_code"><![CDATA[
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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17 cat '$msstatstmt_script' > '$out_r_script' &&
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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18 Rscript '$msstatstmt_script'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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19 && cat msstats*.log > '$out_msstats_log'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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20 && cat msstatstmt.log > '$out_msstatstmt_log'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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21 ]]></command>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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22 <configfiles>
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23 <configfile name="msstatstmt_script"><![CDATA[
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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24 library(MSstatsTMT, warn.conflicts = F, quietly = T, verbose = F)
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25
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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26 #if $input.input_src == 'MSstatsTMT'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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27 input <- read.table("$input.msstatstmt_input", sep="\t", header=TRUE)
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28
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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29 #elif $input.input_src == 'MaxQuant'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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30 proteinGroups.mq <- read.table("$input.proteinGroups", sep="\t", header=TRUE)
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31 evidence.mq <- read.table("$input.evidence", sep="\t", header=TRUE)
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32 annotation.mq <- read.table("$input.annotation", sep="\t", header=TRUE)
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33
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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34 input <- MaxQtoMSstatsTMTFormat(evidence = evidence.mq,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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35 proteinGroups = proteinGroups.mq,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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36 annotation = annotation.mq,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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37 which.proteinid = "$input.proteinID",
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38 rmProt_Only.identified.by.site = $input.input_options.rmProt_Onlyidentifiedbysite,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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39 useUniquePeptide = $input.input_options.useUniquePeptide,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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40 rmPSM_withMissing_withinRun = $input.input_options.rmPSM_withMissing_withinRun,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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41 rmPSM_withfewMea_withinRun = $input.input_options.rmPSM_withfewMea_withinRun,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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42 rmProtein_with1Feature = $input.input_options.rmProtein_with1Feature,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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43 summaryforMultipleRows = $input.input_options.summaryforMultipleRows)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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44
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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45 #elif $input.input_src == 'OpenMS'
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46 input.oms <- read.table("$input.oms_input", sep="\t", header=TRUE)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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47
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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48 input <- OpenMStoMSstatsTMTFormat(input.oms,
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49 useUniquePeptide = $input.input_options.useUniquePeptide,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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50 rmPSM_withMissing_withinRun = $input.input_options.rmPSM_withMissing_withinRun,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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51 rmPSM_withfewMea_withinRun = $input.input_options.rmPSM_withfewMea_withinRun,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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52 rmProtein_with1Feature = $input.input_options.rmProtein_with1Feature,
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53 summaryforMultiplePSMs = $input.input_options.summaryforMultiplePSMs)
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54 #end if
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55
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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56 quant <- proteinSummarization(input,
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57 method = "$proteinSummarization.method",
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58 global_norm = $proteinSummarization.global_norm,
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59 reference_norm = $proteinSummarization.reference_norm,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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60 remove_norm_channel = $proteinSummarization.remove_norm_channel,
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61 remove_empty_channel = $proteinSummarization.remove_empty_channel,
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62 MBimpute = $proteinSummarization.MBimpute,
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63 #if $proteinSummarization.maxQuantileforCensored == ''
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64 maxQuantileforCensored = NULL)
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65 #else
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66 maxQuantileforCensored = $proteinSummarization.maxQuantileforCensored)
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67 #end if
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68
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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69 #for $plot_type in $selected_outputs
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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70 #if $plot_type[-4:] == "Plot"
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71 dataProcessPlotsTMT(input,
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72 quant,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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73 type = '$plot_type',
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74 ylimUp = $out_plots_opt.ylimUp,
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75 ylimDown = $out_plots_opt.ylimDown,
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76 x.axis.size = $out_plots_opt.x_axis_size,
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77 y.axis.size = $out_plots_opt.y_axis_size,
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78 text.size = $out_plots_opt.text_size,
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79 text.angle = $out_plots_opt.text_angle,
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80 legend.size = $out_plots_opt.legend_size,
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diff changeset
81 dot.size.profile = $out_plots_opt.dot_size_profile,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
82 ncol.guide = $out_plots_opt.ncol_guide,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
83 width = $out_plots_opt.width,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
84 height = $out_plots_opt.height,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
85 #if $out_plots_opt.which_Protein.select != 'list'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
86 which.Protein = "$out_plots_opt.which_Protein.select",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
87 #else
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
88 which.Protein = unlist(read.table("$out_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE),
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
89 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
90 originalPlot = $out_plots_opt.originalPlot,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
91 summaryPlot = $out_plots_opt.summaryPlot)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
92 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
93 #end for
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
94
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
95 #if $group.group_comparison == 'true'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
96 #if $group.use_comp_matrix.select == 'true'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
97 comp_matrix <- read.table("$group.use_comp_matrix.comparison_matrix", sep="\t", header=TRUE, check.names=FALSE)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
98
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
99 comparison <- comp_matrix[,-1]
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
100 row.names(comparison) <- as.character(comp_matrix[,1])
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
101 comparison <- as.matrix(comparison[levels(quant\$Condition)])
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
102 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
103
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
104 comparisons <- groupComparisonTMT(data = quant,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
105 #if $group.use_comp_matrix.select == 'true'
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
106 contrast.matrix = comparison,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
107 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
108 moderated = $group.moderated,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
109 adj.method = "$group.adj_method",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
110 remove_norm_channel = $group.remove_norm_channel,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
111 remove_empty_channel = $group.remove_empty_channel)
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
112
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
113 write.table(comparisons,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
114 "ComparisonResult.tsv",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
115 sep = "\t",
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
116 quote = F,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
117 row.names = F,
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
118 dec = ".")
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
119 #end if
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
120 ]]></configfile>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
121 </configfiles>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
122 <inputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
123 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
124 <param name="input_src" type="select" label="Input Source">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
125 <option value="MSstatsTMT">MStatsTMT (11 column format)</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
126 <option value="MaxQuant">MaxQuant</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
127 <option value="OpenMS">OpenMS</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
128 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
129 <when value="MSstatsTMT">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
130 <param name="msstatstmt_input" type="data" format="tabular" label="MStatsTMT (11 column format)"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
131 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
132 <when value="MaxQuant">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
133 <param name="evidence" type="data" format="tabular" label="evidence.txt - feature-level data"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
134 <param name="proteinGroups" type="data" format="tabular" label="proteinGroups.txt" help="It needs to matching protein group ID. If proteinGroups=NULL, use 'Proteins' column in 'evidence.txt'"/>
1
b79d4c961009 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 5ac4f6093606746adb0d40fe4f73871f5934d091"
galaxyp
parents: 0
diff changeset
135 <param name="annotation" type="data" format="tabular" label="annotation.txt" help="Data frame which contains column Run, Fraction, TechRepMixture, Channel, Condition, BioReplicate, Mixture." />
0
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
136 <param name="proteinID" type="select" label="Select Protein ID in evidence.txt">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
137 <option value="Proteins">Protein column</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
138 <option value="Leading.razor.protein">Leading razor protein column</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
139 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
140 <section name="input_options" title="MaxQtoMSstatsTMTFormat Options" expanded="false">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
141 <param name="rmProt_Onlyidentifiedbysite" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove proteins only identified by site" help="Yes will remove proteins with ’+’ in ’Only.identified.by.site’ column from proteinGroups.txt, which was identified only by a modification site. No is the default." />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
142 <expand macro="input_options_shared"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
143 <param name="summaryforMultipleRows" type="select" label="Summary for multiple rows" help="When there are multiple measurements for certain feature in certain run, select the feature with the largest summation or maximal value.">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
144 <option value="max">max</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
145 <option value="sum" selected="true">sum</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
146 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
147 </section>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
148 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
149 <when value="OpenMS">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
150 <param name="oms_input" type="data" format="tabular" label="OpenMS input"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
151 <section name="input_options" title="OpenMStoMSstatsTMTFormat Options" expanded="false">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
152 <expand macro="input_options_shared"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
153 <param name="summaryforMultiplePSMs" type="select" label="Summary for multiple PSMs" help="When there are multiple measurements for certain feature in certain run, select the feature with the largest summation or maximal value.">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
154 <option value="max">max</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
155 <option value="sum" selected="true">sum</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
156 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
157 </section>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
158 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
159 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
160 <section name="proteinSummarization" title="proteinSummarization Options" expanded="false">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
161 <param name="method" type="select" multiple="false" label="Select method">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
162 <option value="msstats" selected="true">msstats</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
163 <option value="MedianPolish">MedianPolish</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
164 <option value="Median">Median</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
165 <option value="LogSum">LogSum</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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166 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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diff changeset
167 <param name="global_norm" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Global median normalization" help="Global median normalization on peptide level data (equalizing the medians across all the channels and MS runs). Default is Yes. It will be performed before protein-level summarization."/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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168 <param name="reference_norm" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Reference channel based normalization" help="Reference channel based normalization between MS runs on protein level data. Yes (default) needs at least one reference channel in each MS run, annotated by ’Norm’ in condition column. It will be performed after protein-level summarization. No will not perform this normalization step. If data only has one run, then use No"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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diff changeset
169 <param name="remove_norm_channel" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove ’Norm’ channels from protein level data."/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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170 <param name="remove_empty_channel" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove ’Empty’ channels from protein level data"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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diff changeset
171 <param name="MBimpute" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="MBimpute" help="Only for 'method = msstats'. Yes (default) imputes missing values by accelerated failure time (AFT) model. No uses minimum value to impute the missing value for each peptide precursor ion."/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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172 <param name="maxQuantileforCensored" type="float" optional="true" min="0" max="0.999" value="" label="Maximum quantile for deciding censored missing value" help="We assume missing values are censored. maxQuantileforCensored is maximum quantile for deciding censored missing value, for instance, 0.999. Default is empty"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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173 </section>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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174 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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175 <param name="group_comparison" type="select" label="Compare Groups">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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176 <option value="false">No</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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177 <option value="true">Yes</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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178 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
179 <when value="false"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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180 <when value="true">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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181 <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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182 <param name="select" type="select" label="Use comparison matrix?">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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183 <option value="false">No</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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184 <option value="true">Yes</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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185 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
186 <when value="false"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
187 <when value="true">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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188 <param name="comparison_matrix" type="data" format="tabular" label="Comparison Matrix"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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189 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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190 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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diff changeset
191 <param name="moderated" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Moderate t statistic" help="No (default) uses ordinary t statistic"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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192 <param name="adj_method" type="select" label="Adjusted p value method for multiple comparison">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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193 <option value="holm">holm</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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194 <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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195 <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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196 <option value="bonferroni">bonferroni</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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197 <option value="BH" selected="true">BH</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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198 <option value="BY">BY</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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199 <option value="fdr">fdr</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
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200 <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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diff changeset
201 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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diff changeset
202 <param name="remove_norm_channel" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove ’Norm’ channels from protein level data"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
203 <param name="remove_empty_channel" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove ’Empty’ channels from protein level data"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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diff changeset
204 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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205 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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206 <param name="selected_outputs" type="select" multiple="true" optional="false" label="Select Outputs">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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207 <option value="msstats_log" selected="true">MSstats log</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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208 <option value="msstatstmt_log" selected="true">MSstatsTMT log</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
209 <option value="r_script" selected="false">MSstats Rscript</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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210 <option value="ProfilePlot" selected="false">Profile Plot</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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211 <option value="QCPlot" selected="false">QC Plot</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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diff changeset
212 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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213 <section name="out_plots_opt" title="Plot Output Options" expanded="false">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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214 <param name="ylimUp" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Upper limit for y-axis in the log scale" help="No (Default) for Profile Plot and QC Plot uses the upper limit as rounded off maximum of log2(intensities) after normalization + 3."/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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215 <param name="ylimDown" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Lower limit for y-axis in the log scale" help="No (Default) for Profile Plot and QCPlot uses 0."/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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216 <param name="x_axis_size" type="integer" min="1" value="10" label="Size of x-axis labeling"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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217 <param name="y_axis_size" type="integer" min="1" value="10" label="Size of y-axis labeling"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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218 <param name="text_size" type="integer" min="1" value="4" label="Size of labels represented each condition at the top"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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219 <param name="text_angle" type="integer" min="0" max="360" value="90" label="Angle of labels represented each condition at the top"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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220 <param name="legend_size" type="integer" min="1" value="7" label="Size of legend above Profile plot"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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221 <param name="dot_size_profile" type="integer" min="1" value="2" label="Size of dots in Profile plot"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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222 <param name="ncol_guide" type="integer" min="1" value="5" label="Number of columns for legends at the top of plot"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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223 <param name="width" type="integer" min="1" value="10" label="Width of the saved pdf file"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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224 <param name="height" type="integer" min="1" value="10" label="Height of the saved pdf file"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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225 <conditional name="which_Protein">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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226 <param name="select" type="select" label="Select protein IDs to draw plots">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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227 <option value="all" selected="true">generate all plots for each protein</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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228 <option value="allonly">Option for QC plot: "allonly" will generate one QC plot with all proteins</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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229 <option value="list">Protein IDs as tabular input</option>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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230 </param>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
231 <when value="all"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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diff changeset
232 <when value="allonly"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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233 <when value="list">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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234 <param name="protein_list" type="data" format="tabular" label="List of proteins"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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235 </when>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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236 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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237 <param name="originalPlot" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Draw original profile plots without normalization"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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238 <param name="summaryPlot" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Draw profile plots with protein summarization for each channel and MS run"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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239 </section>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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240 </inputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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241 <outputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
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242 <data name="out_msstats_log" format="txt" label="${tool.name} on ${on_string}: MSstats log">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
243 <filter>'msstats_log' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
244 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
245 <data name="out_msstatstmt_log" format="txt" label="${tool.name} on ${on_string}: MSstatsTMT log">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
246 <filter>'msstatstmt_log' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
247 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
248 <data name="out_r_script" format="txt" label="${tool.name} on ${on_string}: Rscript">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
249 <filter>'r_script' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
250 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
251 <data name="out_profile_plot" from_work_dir="ProfilePlot.pdf" format="pdf" label="${tool.name} on ${on_string}: Profile Plot">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
252 <filter>'ProfilePlot' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
253 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
254 <data name="out_qc_plot" from_work_dir="QCPlot.pdf" format="pdf" label="${tool.name} on ${on_string}: QC Plot">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
255 <filter>'QCPlot' in selected_outputs</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
256 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
257 <data name="out_group_comp" from_work_dir="ComparisonResult.tsv" format="tsv" label="${tool.name} on ${on_string}: Group Comparison">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
258 <filter>group['group_comparison'] == 'true'</filter>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
259 </data>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
260 </outputs>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
261 <tests>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
262 <test expect_num_outputs="5">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
263 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
264 <param name="input_src" value="MSstatsTMT"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
265 <param name="msstatstmt_input" ftype="tabular" value="input.msstatstmt.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
266 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
267 <param name="selected_outputs" value="msstats_log,msstatstmt_log,r_script,ProfilePlot,QCPlot"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
268 <output name="out_msstats_log">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
269 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
270 <has_text text="1 level of Isotope type labeling in this experiment" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
271 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
272 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
273 <output name="out_msstatstmt_log">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
274 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
275 <has_text text="MSstatsTMT - proteinSummarization function" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
276 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
277 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
278 <output name="out_r_script">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
279 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
280 <has_n_lines n="51" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
281 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
282 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
283 <output name="out_profile_plot" file="ProfilePlot.pdf" compare="sim_size"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
284 <output name="out_qc_plot" file="QCPlot.pdf" compare="sim_size"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
285 </test>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
286 <test expect_num_outputs="2">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
287 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
288 <param name="input_src" value="MaxQuant"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
289 <param name="evidence" ftype="tabular" value="evidence.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
290 <param name="annotation" ftype="tabular" value="annotation.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
291 <param name="proteinGroups" ftype="tabular" value="proteinGroups.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
292 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
293 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
294 <param name="group_comparison" value="true"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
295 <conditional name="use_comp_matrix">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
296 <param name="select" value="true"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
297 <param name="comparison_matrix" ftype="tabular" value="comparison_matrix.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
298 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
299 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
300 <param name="selected_outputs" value="ProfilePlot"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
301 <conditional name="which_Protein">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
302 <param name="select" value="list"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
303 <param name="protein_list" ftype="tabular" value="proteinIDs.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
304 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
305 <output name="out_group_comp">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
306 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
307 <has_n_lines n="21" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
308 <has_n_columns n="8" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
309 <has_text text="A0AVT1" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
310 <has_text text="A0AVT1" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
311 <has_text text="O43324" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
312 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
313 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
314 <output name="out_profile_plot" file="ProfilePlot_list.pdf" compare="sim_size"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
315 </test>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
316 <test expect_num_outputs="2">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
317 <conditional name="input">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
318 <param name="input_src" value="OpenMS"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
319 <param name="oms_input" ftype="tabular" value="input.oms.txt"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
320 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
321 <conditional name="group">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
322 <param name="group_comparison" value="true"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
323 </conditional>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
324 <param name="selected_outputs" value="msstats_log"/>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
325 <output name="out_group_comp">
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
326 <assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
327 <has_n_lines n="51" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
328 <has_n_columns n="8" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
329 <has_text text="Long_LF-Short_HF" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
330 <has_text text="sp|O35226|PSMD4_MOUSE" />
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
331 </assert_contents>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
332 </output>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
333 </test>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
334 </tests>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
335 <help><![CDATA[
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
336 MSstatsTMT is an R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It is applicable to isobaric labeling quantitative proteomics, including iTRAQ and TMT data. MSstatsTMT provides functionalities for two types of analysis: 1) Protein summarization based on peptide quantification data and visualization; 2) Model-based group comparison to detect significant changes in abundance.
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
337
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
338 **Notes**
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
339
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
340 - MSstatsTMT 11 column format: For TMT datasets an additional 'Channel' column is required.
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
341
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
342 ::
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
343
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
344 #> ProteinName PeptideSequence
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
345 #> 1 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
346 #> 2 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
347 #> 3 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
348 #> 4 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
349 #> 5 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
350 #> 6 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
351 #> PrecursorCharge PSM Mixture
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
352 #> 1 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
353 #> 2 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
354 #> 3 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
355 #> 4 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
356 #> 5 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
357 #> 6 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
358 #> TechRepMixture Run Channel BioReplicate Condition Intensity
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
359 #> 1 3_3 3_3_3 1 21 Long_HF NA
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
360 #> 2 3_3 3_3_3 2 22 Norm 1068.580
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
361 #> 3 3_3 3_3_3 3 23 Long_M 1508.330
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
362 #> 4 3_3 3_3_3 4 24 Long_HF NA
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
363 #> 5 3_3 3_3_3 5 25 Long_LF 1580.951
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
364 #> 6 3_3 3_3_3 6 26 Long_HF 1820.072
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
365
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
366 For more information please visit the `MSstatsConvert documentation <https://bioconductor.org/packages/devel/bioc/vignettes/MSstatsConvert/inst/doc/msstats_data_format.html>`_
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
367
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
368 - Comparison matrix as tabular file
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
369
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
370 - 1st column: name of comparison
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
371 - additionally one column for each condition that is present in the tabular file. Use 1 and -1 to indicate the conditions to compare and 0 for conditions that are not compared. Multiple groups can be combined by using 0.5.
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
372 - first row contains the names of the groups, they must exactly match the condition name used in the annotation file
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
373 - each additional row represents one comparison
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
374 - Example for a two group comparison
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
375
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
376 ::
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
377
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
378 names groupA groupB
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
379 groupA-groupB 1 -1
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
380
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
381
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
382 - Example for an experiment with 5 groups and 4 different comparisons
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
383
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
384 ::
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
385
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
386 names G1 G2 G3 G4 G5
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
387 G2-G1 -1 1 0 0 0
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
388 G4-G5 0 0 0 1 -1
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
389 G3-G5 0 0 -1 0 1
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
390 G1+G2-G5 0.5 0.5 0 0 -1
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
391
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
392 For additional help please visit the `MSstatsTMT documentation <https://msstats.org/msstatstmt/>`_
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
393 ]]>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
394 </help>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
395 <citations>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
396 <citation type="doi">10.1074/mcp.ra120.002105</citation>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
parents:
diff changeset
397 </citations>
fd3dc69b78ff "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
galaxyp
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diff changeset
398 </tool>