| Previous changeset 3:5667ff6f7a40 (2021-03-12) Next changeset 5:a5e394b36d87 (2021-08-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 0ed9b6032443be289192cb096c4a5694fccd3639" |
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modified:
msstatstmt.xml test-data/comparison_matrix.txt |
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| diff -r 5667ff6f7a40 -r 8375a0035d79 msstatstmt.xml --- a/msstatstmt.xml Fri Mar 12 14:03:17 2021 +0000 +++ b/msstatstmt.xml Mon Jul 26 20:21:27 2021 +0000 |
| [ |
| b'@@ -1,8 +1,8 @@\n <tool id="msstatstmt" name="MSstatsTMT" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">\n <description>protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</description>\n <macros>\n- <token name="@TOOL_VERSION@">1.8.2</token>\n- <token name="@GALAXY_VERSION@">1</token>\n+ <token name="@TOOL_VERSION@">2.0.0</token>\n+ <token name="@GALAXY_VERSION@">0</token>\n <xml name="input_options_shared">\n <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." />\n <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." />\n@@ -16,8 +16,24 @@\n <command detect_errors="exit_code"><![CDATA[\n cat \'$msstatstmt_script\' > \'$out_r_script\' &&\n Rscript \'$msstatstmt_script\'\n- && cat msstats*.log > \'$out_msstats_log\'\n- && cat msstatstmt.log > \'$out_msstatstmt_log\'\n+\n+ && cat MSstatsTMT_summarization_log*.log > \'$out_msstatstmt_sum_log\'\n+ && cat MSstatsTMT_summarization_MSstats*.log > \'$out_msstatstmt_sum_ms\'\n+\n+ #if $input.input_src != \'MSstatsTMT\':\n+ && cat MSstatsTMT_converter_log*.log > \'$out_msstatstmt_conv_log\'\n+ #else:\n+ && echo "MSstatsTMT input. No conversion needed." > \'$out_msstatstmt_conv_log\'\n+ #end if\n+\n+ #if $group.group_comparison == \'true\':\n+ && cat MSstatsTMT_log_groupComparison*.log > \'$out_msstatstmt_group_log\'\n+ && cat MSstats_log*.log > \'$out_msstats_gc_log\'\n+ #else:\n+ && echo "No groupComparison was performed." > \'$out_msstatstmt_group_log\'\n+ && echo "No groupComparison was performed." > \'$out_msstats_gc_log\'\n+ #end if\n+\n ]]></command>\n <configfiles>\n <configfile name="msstatstmt_script"><![CDATA[\n@@ -84,8 +100,7 @@\n \n #for $plot_type in $selected_outputs\n #if $plot_type[-4:] == "Plot"\n- dataProcessPlotsTMT(input,\n- quant,\n+ dataProcessPlotsTMT(quant,\n type = \'$plot_type\',\n ylimUp = $out_plots_opt.adv.ylimUp,\n ylimDown = $out_plots_opt.adv.ylimDown,\n@@ -110,7 +125,7 @@\n originalPlot = $out_plots_opt.adv.originalPlot,\n summaryPlot = $out_plots_opt.adv.summaryPlot)\n #elif $plot_type == "quant"\n- write.table(quant,\n+ write.table(quant\\$ProteinLevelData,\n "Quant.tsv",\n sep = "\\t",\n quote = F,\n@@ -125,7 +140,7 @@\n \n comparison <- comp_matrix[,-1]\n row.names(comparison) <- as.character(comp_matrix[,1])\n- comparison <- as.matrix(comparison[levels(quant\\$Condition)])\n+ comparison <- as.matrix(comparison[levels(quant\\$ProteinLevelData\\$Condition)])\n #end if\n \n comparisons <- groupComparisonTMT(data = quant,\n@@ -137,7 +152,7 @@\n remove_norm_channel = $group.remove_norm_channel,\n remove_empty_channel = $group.remove_empty_channel)\n \n- write.table(comparisons,\n+ write.table(comparisons\\$ComparisonResult,\n "ComparisonResult.tsv",\n sep = "\\t",\n quote = F,\n@@ -146,7 +161,12 @@\n \n #for $plot_type in $group.selected_group_outputs\n #if $plot_type == "VolcanoPlot" or $plot_type == "Heatmap" or $plot_type == "ComparisonPlot"\n- groupComparisonPlots(data = comparisons,\n+\n+ ## Workaround for missing option "MSstatsLog" (get'..b' </data>\n <data name="out_r_script" format="txt" label="${tool.name} on ${on_string}: Rscript">\n <filter>\'r_script\' in selected_outputs</filter>\n@@ -415,31 +447,31 @@\n </data>\n </outputs>\n <tests>\n- <test expect_num_outputs="5">\n+ <test expect_num_outputs="6">\n <conditional name="input">\n <param name="input_src" value="MSstatsTMT"/>\n <param name="msstatstmt_input" ftype="tabular" value="input.msstatstmt.txt"/>\n </conditional>\n- <param name="selected_outputs" value="msstats_log,msstatstmt_log,r_script,ProfilePlot,QCPlot"/>\n- <output name="out_msstats_log">\n+ <param name="selected_outputs" value="msstatstmt_conv_log,msstatstmt_sum_ms,msstatstmt_sum_log,r_script,ProfilePlot,QCPlot"/>\n+ <output name="out_msstatstmt_sum_ms">\n <assert_contents>\n- <has_text text="1 level of Isotope type labeling in this experiment" />\n+ <has_text text="MSstats - dataProcess function" />\n </assert_contents>\n </output>\n- <output name="out_msstatstmt_log">\n+ <output name="out_msstatstmt_sum_log">\n <assert_contents>\n <has_text text="MSstatsTMT - proteinSummarization function" />\n </assert_contents>\n </output>\n <output name="out_r_script">\n <assert_contents>\n- <has_n_lines n="52" />\n+ <has_n_lines n="50" />\n </assert_contents>\n </output>\n <output name="out_profile_plot" file="ProfilePlot.pdf" compare="sim_size"/>\n <output name="out_qc_plot" file="QCPlot.pdf" compare="sim_size"/>\n </test>\n- <test expect_num_outputs="4">\n+ <test expect_num_outputs="6">\n <conditional name="input">\n <param name="input_src" value="MaxQuant"/>\n <param name="evidence" ftype="tabular" value="evidence.txt"/>\n@@ -454,7 +486,7 @@\n </conditional>\n <param name="selected_group_outputs" value="comparison_result,VolcanoPlot,ComparisonPlot"/>\n </conditional>\n- <param name="selected_outputs" value="ProfilePlot"/>\n+ <param name="selected_outputs" value="ProfilePlot,msstatstmt_group_log,msstats_gc_log"/>\n <conditional name="which_Protein">\n <param name="select" value="list"/>\n <param name="protein_list" ftype="tabular" value="proteinIDs.txt"/>\n@@ -484,14 +516,14 @@\n <param name="selected_outputs" value="r_script"/>\n <output name="out_r_script">\n <assert_contents>\n- <has_n_lines n="58" />\n+ <has_n_lines n="61" />\n </assert_contents>\n </output>\n <output name="out_group_comp">\n <assert_contents>\n <has_n_lines n="51" />\n <has_n_columns n="8" />\n- <has_text text="Long_LF-Short_HF" />\n+ <has_text text="Long_LF vs Short_HF" />\n <has_text text="sp|O35226|PSMD4_MOUSE" />\n </assert_contents>\n </output>\n@@ -543,7 +575,7 @@\n #> 4 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR\n #> 5 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR\n #> 6 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR\n- #> PrecursorCharge PSM Mixture\n+ #> Charge PSM Mixture\n #> 1 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3\n #> 2 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3\n #> 3 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3\n' |
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| diff -r 5667ff6f7a40 -r 8375a0035d79 test-data/comparison_matrix.txt --- a/test-data/comparison_matrix.txt Fri Mar 12 14:03:17 2021 +0000 +++ b/test-data/comparison_matrix.txt Mon Jul 26 20:21:27 2021 +0000 |
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| @@ -2,4 +2,4 @@ 0.5-0.125 -1 1 0 0 0.667-0.5 0 -1 1 0 1-0.667 0 0 -1 1 -0.125-1 1 0 0 -1 \ No newline at end of file +0.125-1 1 0 0 -1 |