Mercurial > repos > galaxyp > msstatstmt
changeset 4:8375a0035d79 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639"
| author | galaxyp |
|---|---|
| date | Mon, 26 Jul 2021 20:21:27 +0000 |
| parents | 5667ff6f7a40 |
| children | a5e394b36d87 |
| files | msstatstmt.xml test-data/comparison_matrix.txt |
| diffstat | 2 files changed, 60 insertions(+), 28 deletions(-) [+] |
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--- a/msstatstmt.xml Fri Mar 12 14:03:17 2021 +0000 +++ b/msstatstmt.xml Mon Jul 26 20:21:27 2021 +0000 @@ -1,8 +1,8 @@ <tool id="msstatstmt" name="MSstatsTMT" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</description> <macros> - <token name="@TOOL_VERSION@">1.8.2</token> - <token name="@GALAXY_VERSION@">1</token> + <token name="@TOOL_VERSION@">2.0.0</token> + <token name="@GALAXY_VERSION@">0</token> <xml name="input_options_shared"> <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." /> <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." /> @@ -16,8 +16,24 @@ <command detect_errors="exit_code"><![CDATA[ cat '$msstatstmt_script' > '$out_r_script' && Rscript '$msstatstmt_script' - && cat msstats*.log > '$out_msstats_log' - && cat msstatstmt.log > '$out_msstatstmt_log' + + && cat MSstatsTMT_summarization_log*.log > '$out_msstatstmt_sum_log' + && cat MSstatsTMT_summarization_MSstats*.log > '$out_msstatstmt_sum_ms' + + #if $input.input_src != 'MSstatsTMT': + && cat MSstatsTMT_converter_log*.log > '$out_msstatstmt_conv_log' + #else: + && echo "MSstatsTMT input. No conversion needed." > '$out_msstatstmt_conv_log' + #end if + + #if $group.group_comparison == 'true': + && cat MSstatsTMT_log_groupComparison*.log > '$out_msstatstmt_group_log' + && cat MSstats_log*.log > '$out_msstats_gc_log' + #else: + && echo "No groupComparison was performed." > '$out_msstatstmt_group_log' + && echo "No groupComparison was performed." > '$out_msstats_gc_log' + #end if + ]]></command> <configfiles> <configfile name="msstatstmt_script"><![CDATA[ @@ -84,8 +100,7 @@ #for $plot_type in $selected_outputs #if $plot_type[-4:] == "Plot" - dataProcessPlotsTMT(input, - quant, + dataProcessPlotsTMT(quant, type = '$plot_type', ylimUp = $out_plots_opt.adv.ylimUp, ylimDown = $out_plots_opt.adv.ylimDown, @@ -110,7 +125,7 @@ originalPlot = $out_plots_opt.adv.originalPlot, summaryPlot = $out_plots_opt.adv.summaryPlot) #elif $plot_type == "quant" - write.table(quant, + write.table(quant\$ProteinLevelData, "Quant.tsv", sep = "\t", quote = F, @@ -125,7 +140,7 @@ comparison <- comp_matrix[,-1] row.names(comparison) <- as.character(comp_matrix[,1]) - comparison <- as.matrix(comparison[levels(quant\$Condition)]) + comparison <- as.matrix(comparison[levels(quant\$ProteinLevelData\$Condition)]) #end if comparisons <- groupComparisonTMT(data = quant, @@ -137,7 +152,7 @@ remove_norm_channel = $group.remove_norm_channel, remove_empty_channel = $group.remove_empty_channel) - write.table(comparisons, + write.table(comparisons\$ComparisonResult, "ComparisonResult.tsv", sep = "\t", quote = F, @@ -146,7 +161,12 @@ #for $plot_type in $group.selected_group_outputs #if $plot_type == "VolcanoPlot" or $plot_type == "Heatmap" or $plot_type == "ComparisonPlot" - groupComparisonPlots(data = comparisons, + + ## Workaround for missing option "MSstatsLog" (getOption("MSstatsLog") returns NULL) + MSstatsConvert::MSstatsLogsSettings() + ############################################# + + groupComparisonPlots(data = comparisons\$ComparisonResult, type = "$plot_type", sig = $group.comparison_plots_opt.sig, #if $group.comparison_plots_opt.FCcutoff: @@ -374,8 +394,11 @@ </when> </conditional> <param name="selected_outputs" type="select" multiple="true" optional="false" label="Select Outputs"> - <option value="msstats_log" selected="true">MSstats log</option> - <option value="msstatstmt_log" selected="true">MSstatsTMT log</option> + <option value="msstatstmt_conv_log" selected="false">MSstatsTMT converter log</option> + <option value="msstatstmt_sum_log" selected="true">MSstatsTMT summarization log</option> + <option value="msstatstmt_sum_ms" selected="true">MSstatsTMT summarization MSstats</option> + <option value="msstatstmt_group_log" selected="false">MSstatsTMT groupComparison log</option> + <option value="msstats_gc_log" selected="false">MSstats log (groupComparison)</option> <option value="r_script" selected="false">MSstats Rscript</option> <option value="quant" selected="true">Protein abundance</option> <option value="ProfilePlot" selected="false">Profile Plot</option> @@ -383,11 +406,20 @@ </param> </inputs> <outputs> - <data name="out_msstats_log" from_work_dir="msstats.log" format="txt" label="${tool.name} on ${on_string}: MSstats log"> - <filter>'msstats_log' in selected_outputs</filter> + <data name="out_msstatstmt_conv_log" from_work_dir="MSstatsTMT_converter_log.log" format="txt" label="${tool.name} on ${on_string}: MSstatsTMT converter log"> + <filter>'msstatstmt_conv_log' in selected_outputs</filter> + </data> + <data name="out_msstatstmt_sum_log" from_work_dir="MSstatsTMT_summarization_log.log" format="txt" label="${tool.name} on ${on_string}: MSstatsTMT summarization log"> + <filter>'msstatstmt_sum_log' in selected_outputs</filter> </data> - <data name="out_msstatstmt_log" from_work_dir="msstatstmt.log" format="txt" label="${tool.name} on ${on_string}: MSstatsTMT log"> - <filter>'msstatstmt_log' in selected_outputs</filter> + <data name="out_msstatstmt_sum_ms" from_work_dir="MSstatsTMT_summarization_MSstats.log" format="txt" label="${tool.name} on ${on_string}: MSstatsTMT summarization MSstats"> + <filter>'msstatstmt_sum_ms' in selected_outputs</filter> + </data> + <data name="out_msstatstmt_group_log" from_work_dir="MSstatsTMT_log_groupComparison.log" format="txt" label="${tool.name} on ${on_string}: MSstatsTMT groupComparison log"> + <filter>'msstatstmt_group_log' in selected_outputs</filter> + </data> + <data name="out_msstats_gc_log" from_work_dir="MSstats_log.log" format="txt" label="${tool.name} on ${on_string}: MSstats log (groupComparison)"> + <filter>'msstats_gc_log' in selected_outputs</filter> </data> <data name="out_r_script" format="txt" label="${tool.name} on ${on_string}: Rscript"> <filter>'r_script' in selected_outputs</filter> @@ -415,31 +447,31 @@ </data> </outputs> <tests> - <test expect_num_outputs="5"> + <test expect_num_outputs="6"> <conditional name="input"> <param name="input_src" value="MSstatsTMT"/> <param name="msstatstmt_input" ftype="tabular" value="input.msstatstmt.txt"/> </conditional> - <param name="selected_outputs" value="msstats_log,msstatstmt_log,r_script,ProfilePlot,QCPlot"/> - <output name="out_msstats_log"> + <param name="selected_outputs" value="msstatstmt_conv_log,msstatstmt_sum_ms,msstatstmt_sum_log,r_script,ProfilePlot,QCPlot"/> + <output name="out_msstatstmt_sum_ms"> <assert_contents> - <has_text text="1 level of Isotope type labeling in this experiment" /> + <has_text text="MSstats - dataProcess function" /> </assert_contents> </output> - <output name="out_msstatstmt_log"> + <output name="out_msstatstmt_sum_log"> <assert_contents> <has_text text="MSstatsTMT - proteinSummarization function" /> </assert_contents> </output> <output name="out_r_script"> <assert_contents> - <has_n_lines n="52" /> + <has_n_lines n="50" /> </assert_contents> </output> <output name="out_profile_plot" file="ProfilePlot.pdf" compare="sim_size"/> <output name="out_qc_plot" file="QCPlot.pdf" compare="sim_size"/> </test> - <test expect_num_outputs="4"> + <test expect_num_outputs="6"> <conditional name="input"> <param name="input_src" value="MaxQuant"/> <param name="evidence" ftype="tabular" value="evidence.txt"/> @@ -454,7 +486,7 @@ </conditional> <param name="selected_group_outputs" value="comparison_result,VolcanoPlot,ComparisonPlot"/> </conditional> - <param name="selected_outputs" value="ProfilePlot"/> + <param name="selected_outputs" value="ProfilePlot,msstatstmt_group_log,msstats_gc_log"/> <conditional name="which_Protein"> <param name="select" value="list"/> <param name="protein_list" ftype="tabular" value="proteinIDs.txt"/> @@ -484,14 +516,14 @@ <param name="selected_outputs" value="r_script"/> <output name="out_r_script"> <assert_contents> - <has_n_lines n="58" /> + <has_n_lines n="61" /> </assert_contents> </output> <output name="out_group_comp"> <assert_contents> <has_n_lines n="51" /> <has_n_columns n="8" /> - <has_text text="Long_LF-Short_HF" /> + <has_text text="Long_LF vs Short_HF" /> <has_text text="sp|O35226|PSMD4_MOUSE" /> </assert_contents> </output> @@ -543,7 +575,7 @@ #> 4 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR #> 5 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR #> 6 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR - #> PrecursorCharge PSM Mixture + #> Charge PSM Mixture #> 1 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3 #> 2 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3 #> 3 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3