| Previous changeset 2:782bd55b000b (2021-02-27) Next changeset 4:8375a0035d79 (2021-07-26) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa" |
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modified:
msstatstmt.xml test-data/MSstats_group_ComparisonPlot.pdf test-data/MSstats_group_Heatmap.pdf test-data/MSstats_group_VolcanoPlot.pdf test-data/ProfilePlot.pdf test-data/ProfilePlot_list.pdf test-data/QCPlot.pdf |
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added:
test-data/ProfilePlot_allonly.pdf |
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| diff -r 782bd55b000b -r 5667ff6f7a40 msstatstmt.xml --- a/msstatstmt.xml Sat Feb 27 10:54:25 2021 +0000 +++ b/msstatstmt.xml Fri Mar 12 14:03:17 2021 +0000 |
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| @@ -99,7 +99,11 @@ width = $out_plots_opt.width, height = $out_plots_opt.height, #if $out_plots_opt.which_Protein.select != 'list' + #if $out_plots_opt.which_Protein.select == "allonly" and $plot_type == "ProfilePlot" + which.Protein = "all", + #else which.Protein = "$out_plots_opt.which_Protein.select", + #end if #else which.Protein = unlist(read.table("$out_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE), #end if @@ -186,13 +190,13 @@ <inputs> <conditional name="input"> <param name="input_src" type="select" label="Input Source"> - <option value="MSstatsTMT">MStatsTMT (11 column format)</option> + <option value="MSstatsTMT">MSstatsTMT (11 column format)</option> <option value="MaxQuant">MaxQuant</option> <option value="OpenMS">OpenMS</option> <option value="PD">Proteome Discoverer</option> </param> <when value="MSstatsTMT"> - <param name="msstatstmt_input" type="data" format="tabular" label="MStatsTMT (11 column format)"/> + <param name="msstatstmt_input" type="data" format="tabular" label="MSstatsTMT (11 column format)"/> </when> <when value="MaxQuant"> <param name="evidence" type="data" format="tabular" label="evidence.txt - feature-level data"/> @@ -509,6 +513,19 @@ </assert_contents> </output> </test> + <test expect_num_outputs="1"> + <conditional name="input"> + <param name="input_src" value="MaxQuant"/> + <param name="evidence" ftype="tabular" value="evidence.txt"/> + <param name="annotation" ftype="tabular" value="annotation.txt"/> + <param name="proteinGroups" ftype="tabular" value="proteinGroups.txt"/> + </conditional> + <param name="selected_outputs" value="ProfilePlot"/> + <conditional name="which_Protein"> + <param name="select" value="allonly"/> + </conditional> + <output name="out_profile_plot" file="ProfilePlot_allonly.pdf" compare="sim_size"/> + </test> </tests> <help><![CDATA[ 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. |
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