# HG changeset patch
# User galaxyp
# Date 1628280379 0
# Node ID 28434abe6c5c93b667373ac81f628b8ff890dab4
# Parent  593839e1f2c399ce4295497e2f8632f813e0e3e4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3"

diff -r 593839e1f2c3 -r 28434abe6c5c msstats.xml
--- a/msstats.xml	Thu Feb 25 08:41:37 2021 +0000
+++ b/msstats.xml	Fri Aug 06 20:06:19 2021 +0000
@@ -1,7 +1,7 @@
-<tool id="msstats" name="MSstats" version="@VERSION@.1">
+<tool id="msstats" name="MSstats" version="@VERSION@.0">
     <description>statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry</description>
     <macros>
-        <token name="@VERSION@">3.22.0</token>
+        <token name="@VERSION@">4.0.0</token>
         <xml name="useUniquePeptide">
             <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove peptides that are assigned for more than one proteins"/>
         </xml>
@@ -28,7 +28,6 @@
     <command detect_errors="exit_code"><![CDATA[
         cat '$msstats_script' > '$r_script' &&
         Rscript '$msstats_script'
-        && cat msstats*.log > '$log'
     ]]></command>
     <configfiles>
         <configfile name="msstats_script"><![CDATA[
@@ -66,7 +65,10 @@
                            fewMeasurements="$input.input_options.fewMeasurements", 
                            removeMpeptides=$input.input_options.removeMpeptides,
                            removeOxidationMpeptides=$input.input_options.removeOxidationMpeptides,
-                           removeProtein_with1Peptide=$input.input_options.removeProtein_with1Peptide)
+                           removeProtein_with1Peptide=$input.input_options.removeProtein_with1Peptide,
+                           use_log_file = TRUE,
+                           append = TRUE,
+                           log_file_pat = "log.txt")
 
 #elif $input.input_src == 'OpenMS'
 
@@ -91,7 +93,10 @@
                              useUniquePeptide=$input.input_options.useUniquePeptide, 
                              summaryforMultipleRows=$input.input_options.summaryforMultipleRows, 
                              fewMeasurements="$input.input_options.fewMeasurements", 
-                             removeProtein_with1Feature=$input.input_options.removeProtein_with1Feature)
+                             removeProtein_with1Feature=$input.input_options.removeProtein_with1Feature,
+                             use_log_file = TRUE,
+                             append = TRUE,
+                             log_file_pat = "log.txt")
 
 
 #elif $input.input_src == 'OpenSWATH'
@@ -114,8 +119,11 @@
                                 useUniquePeptide=$input.input_options.useUniquePeptide,
                                 fewMeasurements="$input.input_options.fewMeasurements",
                                 removeProtein_with1Feature=$input.input_options.removeProtein_with1Feature,
-                                summaryforMultipleRows=$input.input_options.summaryforMultipleRows)
-
+                                summaryforMultipleRows=$input.input_options.summaryforMultipleRows,
+                                use_log_file = TRUE,
+                                append = TRUE,
+                                log_file_pat = "log.txt")
+		                
 #elif $input.input_src == 'Skyline'
 
   #if $input.skyline_input.is_of_type('csv')
@@ -142,7 +150,10 @@
 				useUniquePeptide = $input.input_options.useUniquePeptide,
 				fewMeasurements="$input.input_options.fewMeasurements",
 				removeOxidationMpeptides = $input.input_options.removeOxidationMpeptides,
-				removeProtein_with1Feature = $input.input_options.removeProtein_with1Feature)
+				removeProtein_with1Feature = $input.input_options.removeProtein_with1Feature,
+				use_log_file = TRUE,
+				append = TRUE,
+		                log_file_pat = "log.txt")
 
 #end if
 
@@ -152,7 +163,6 @@
                           #if $dp_options.norm.normalization == 'globalStandards'
                           nameStandards=c($dp_options.norm.nameStandards),
                           #end if
-                          fillIncompleteRows=$dp_options.fillIncompleteRows,
                           featureSubset="$dp_options.features.featureSubset",
                           #if $dp_options.features.featureSubset == 'topN'
                           n_top_feature=$dp_options.features.n_top_feature,
@@ -173,23 +183,26 @@
                           #else
                           censoredInt="$dp_options.censoredInt",
                           #end if
-                          cutoffCensored="$dp_options.cutoffCensored",
                           #if $dp_options.maxQuantileforCensored == ''
-                          maxQuantileforCensored = NULL)
+                          maxQuantileforCensored = NULL,
                           #else
-                          maxQuantileforCensored = $dp_options.maxQuantileforCensored)
+                          maxQuantileforCensored = $dp_options.maxQuantileforCensored,
                           #end if
+                          use_log_file = TRUE,
+                          append = TRUE,
+                          log_file_pat = "log.txt")
+                          
 
 #if 'raw_data' in $dp_options.selected_outputs
 write.table(raw, "raw.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
 #end if
 
-#if 'processed_data' in $dp_options.selected_outputs
-write.table(processed_data\$ProcessedData, "ProcessedData.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
+#if 'featurelevel_data' in $dp_options.selected_outputs
+write.table(processed_data\$FeatureLevelData, "featurelevelData.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
 #end if
 
-#if 'runlevel_data' in $dp_options.selected_outputs
-write.table(processed_data\$RunlevelData, "RunlevelData.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
+#if 'proteinlevel_data' in $dp_options.selected_outputs
+write.table(processed_data\$ProteinLevelData, "proteinlevelData.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
 #end if
 
 #for $plot_type in $dp_options.out_plots_opt.selected_vis_outputs
@@ -217,35 +230,40 @@
                             dot.size.condition = $dp_options.out_plots_opt.proc_plots_advanced.dot_size_condition,
                             width = $dp_options.out_plots_opt.width,
                             height = $dp_options.out_plots_opt.height,
-                            #if $dp_options.out_plots_opt.which_Protein.select != 'list'
-                            which.Protein = "$dp_options.out_plots_opt.which_Protein.select",
+                            #if $dp_options.out_plots_opt.which_Protein.select == 'list'
+                                which.Protein = unlist(read.table("$dp_options.out_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE),
+                            #elif $dp_options.out_plots_opt.which_Protein.select == 'allonly'
+                            	#if $plot_type == "QCPlot"           
+                                    which.Protein = "allonly",
+                                #else 
+                                    which.Protein = "all",
+                                #end if
                             #else
-                            which.Protein = unlist(read.table("$dp_options.out_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE),
+                                which.Protein = "all",
                             #end if
                             remove_uninformative_feature_outlier = $dp_options.out_plots_opt.proc_plots_advanced.remove_uninformative_feature_outlier,
                             address="MSStats_only_")
-
     #end if
 #end for
 
 ## Quantifiaction
 #if 'quant_sample_matrix' in $dp_options.selected_outputs
-sampleQuantMatrix <- quantification(processed_data,  type="Sample")
+sampleQuantMatrix <- quantification(processed_data,  type="Sample", use_log_file = TRUE, append = TRUE, log_file_pat = "log.txt")
 write.table(sampleQuantMatrix, "SampleQuantificationMatrix.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
 #end if
 
 #if 'quant_sample_long' in $dp_options.selected_outputs
-sampleQuantLong <- quantification(processed_data,  type="Sample", format="long")
+sampleQuantLong <- quantification(processed_data,  type="Sample", format="long", use_log_file = TRUE, append = TRUE,  log_file_pat = "log.txt")
 write.table(sampleQuantLong, "SampleQuantificationLong.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
 #end if
 
 #if 'quant_group_matrix' in $dp_options.selected_outputs
-groupQuantMatrix <- quantification(processed_data,  type="Group")
+groupQuantMatrix <- quantification(processed_data,  type="Group", use_log_file = TRUE, append = TRUE,  log_file_pat = "log.txt")
 write.table(groupQuantMatrix, "GroupQuantificationMatrix.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
 #end if
 
 #if 'quant_group_long' in $dp_options.selected_outputs
-groupQuantLong <- quantification(processed_data,  type="Group", format="long")
+groupQuantLong <- quantification(processed_data,  type="Group", format="long", use_log_file = TRUE, append = TRUE,  log_file_pat = "log.txt")
 write.table(groupQuantLong, "GroupQuantificationLong.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
 #end if
 
@@ -261,16 +279,16 @@
 ## first columns contains comparison names, use as row name
 comparison <- comp_matrix[,-1]
 row.names(comparison) <- as.character(comp_matrix[,1])
+
 ## order of conditions has to be the same as they appear in the levels function
-comparison <- as.matrix(comparison[levels(processed_data\$ProcessedData\$GROUP_ORIGINAL)])
+comparison <- as.matrix(comparison[levels(processed_data\$FeatureLevelData\$GROUP)])
 
 ## perform group comparison
-comparisons <- groupComparison(contrast.matrix = comparison, data = processed_data)
+comparisons <- groupComparison(contrast.matrix = comparison, data = processed_data, use_log_file = TRUE, append = TRUE, log_file_pat = "log.txt")
 
-print(comparisons\$fittedmodel)
-  #if 'fittedmodel' in $group.select_outputs
-capture.output(print(comparisons\$fittedmodel), file="ComparisonFittedModel.txt")
-  #end if
+#if 'fittedmodel' in $group.select_outputs
+    capture.output(print(comparisons\$FittedModel), file="ComparisonFittedModel.txt")
+#end if
 
 
   #if 'comparison_result' in $group.select_outputs
@@ -292,8 +310,6 @@
 				type = "$plot_type",
 				axis.size = $group.comparison_plots_opt.comparison_vis_options.axis_size,
 				dot.size = $group.comparison_plots_opt.comparison_vis_options.dot_size,
-				text.size = $group.comparison_plots_opt.comparison_vis_options.text_size,
-				legend.size = $group.comparison_plots_opt.comparison_vis_options.legend_size,
 				width = $group.comparison_plots_opt.width,
 				height = $group.comparison_plots_opt.height,
 				#if $group.comparison_plots_opt.which_Protein.select != 'list'
@@ -424,8 +440,8 @@
 		<option value="log" selected="true">MSstats log</option>
 		<option value="r_script" selected="false">MSstats Rscript</option>
 		<option value="raw_data" selected="true">MSstats RawData</option>
-		<option value="processed_data" selected="true">MSstats ProcessedData</option>
-		<option value="runlevel_data" selected="false">MSstats RunlevelData</option>
+		<option value="featurelevel_data" selected="true">MSstats FeatureLevelData</option>
+		<option value="proteinlevel_data" selected="false">MSstats ProteinLevelData</option>
 		<option value="quant_sample_matrix" selected="false">Sample Quantification Matrix Table</option>
 		<option value="quant_sample_long" selected="false">Sample Quantification Long Table</option>
 		<option value="quant_group_matrix" selected="true">Group Quantification Matrix Table</option>
@@ -452,7 +468,6 @@
                 </when>
                 <when value="FALSE"/>
             </conditional>
-            <param name="fillIncompleteRows" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Fill Incomplete Rows" help="If the input dataset has incomplete rows, 'Yes' (default) adds the rows with intensity value=NA for missing peaks. 'No' reports error message with list of features which have incomplete rows"/>
             <conditional name="features">
                 <param name="featureSubset" type="select" label="Feature Subset">
                     <option value="all" selected="true">Use all features that the data set has</option>
@@ -486,12 +501,7 @@
                 <help>The processing tools report missing values differently. This option is for distinguish which value should be considered as missing, and further whether it is censored or at random. Skyline and OpenSWATH input should use '0'. MaxQuant input should use 'NA'</help>
                 <option value="NA" selected="true">NA - Assume that all 'NA's in 'Intensity' column are censored</option>
                 <option value="0">0 - Use zero intensities '0' as censored intensity</option>
-                <option value="NULL">NULL - Assume all NA intensites are randomly missing</option>
-            </param>
-            <param name="cutoffCensored" type="select" label="Cutoff value for censoring">
-                <option value="minFeature" selected="true">minimum value for each feature</option>
-                <option value="minRun">minimum value for each run</option>
-                <option value="minFeatureNRun">smallest between minimum value of corresponding feature and minimum value of corresponding run</option>
+                <!--option value="NULL">NULL - Assume all NA intensites are randomly missing</option-->
             </param>
             <param name="maxQuantileforCensored" type="float" optional="true" value="0.999" min="0" max="1.0" label="Maximum quantile for deciding censored missing values." help="If you don't want to apply the threshold of noise intensity in your data, remove the value (empty field)"/>
             
@@ -623,8 +633,8 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="log" format="txt" label="${tool.name} on ${on_string}: MSstats log">
-            <filter>'log' in in dp_options['selected_outputs']</filter>
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="log.txt">
+            <filter>'log' in dp_options['selected_outputs']</filter>
         </data>
         <data name="r_script" format="txt" label="${tool.name} on ${on_string}: Rscript">
             <filter>'r_script' in dp_options['selected_outputs']</filter>
@@ -632,14 +642,14 @@
         <data name="raw_data" format="tabular" label="${tool.name} on ${on_string}: RawData" from_work_dir="raw.tsv">
             <filter>'raw_data' in dp_options['selected_outputs']</filter>
         </data>
-        <data name="processed_data" format="tabular" label="${tool.name} on ${on_string}: ProcessedData" from_work_dir="ProcessedData.tsv">
-            <filter>'processed_data' in dp_options['selected_outputs']</filter>
+        <data name="featurelevel_data" format="tabular" label="${tool.name} on ${on_string}: FeatureLevelData" from_work_dir="featurelevelData.tsv">
+            <filter>'featurelevel_data' in dp_options['selected_outputs']</filter>
             <!--actions>
                 <action name="column_names" type="metadata" default="PROTEIN,PEPTIDE,TRANSITION,FEATURE,LABEL,GROUP_ORIGINAL,SUBJECT_ORIGINAL,RUN,GROUP,SUBJECT,INTENSITY,SUBJECT_NESTED,ABUNDANCE,FRACTION,originalRUN,censored" />
             </actions-->
         </data>
-        <data name="runlevel_data" format="tabular" label="${tool.name} on ${on_string}: RunlevelData" from_work_dir="RunlevelData.tsv">
-            <filter>'runlevel_data' in dp_options['selected_outputs']</filter>
+        <data name="proteinlevel_data" format="tabular" label="${tool.name} on ${on_string}: ProteinLevelData" from_work_dir="proteinlevelData.tsv">
+            <filter>'proteinlevel_data' in dp_options['selected_outputs']</filter>
             <!--actions>
                <action name="column_names" type="metadata" default="RUN,Protein,LogIntensities,NumMeasuredFeature,MissingPercentage,more50missing,NumImputedFeature,originalRUN,GROUP,GROUP_ORIGINAL,SUBJECT_ORIGINAL,SUBJECT_NESTED,SUBJECT" />
             </actions-->
@@ -706,17 +716,17 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="6">
             <conditional name="input">
                 <param name="input_src" value="MSstats"/>
                 <param name="msstats_input" ftype="csv" value="msstats_testfile.txt"/>
             </conditional>
-            <param name="selected_outputs" value="raw_data,processed_data,quant_sample_matrix,quant_group_long"/>
+            <param name="selected_outputs" value="raw_data,featurelevel_data,quant_sample_matrix,quant_group_long"/>
             <param name="selected_vis_outputs" value="ProfilePlot,profile_wsum_plot"/>
-            <output name="processed_data">
+            <output name="featurelevel_data">
                 <assert_contents>
-                    <has_text text="D.GPLTGTYR" />
-                    <has_n_columns n="16" />
+                    <has_text text="-.PHSHPALTPEQK_347_NA_347_NA" />
+                    <has_n_columns n="15" />
                     <has_n_lines n="2071" />
                 </assert_contents>
             </output>
@@ -735,10 +745,10 @@
                 </assert_contents>
             </output>
             <output name="ProfilePlot" file="MSstats ProfilePlot.pdf" compare="sim_size"/>
-            <output name="profile_wsum_plot" file="profile_wsum_plot.pdf" compare="sim_size"/>                     
+            <output name="profile_wsum_plot" file="profile_wsum_plot.pdf" compare="sim_size"/>                             
         </test>
 
-        <test>
+        <test expect_num_outputs="6">
             <conditional name="input">
                 <param name="input_src" value="MSstats"/>
                 <param name="msstats_input" ftype="tabular" value="msstats_testfile.tsv"/>
@@ -749,31 +759,31 @@
             </conditional>
             <param name="select_outputs" value="model_qc"/>
             <param name="select_comparison_plots" value="ResidualPlots"/>
-            <output name="processed_data">
+            <output name="featurelevel_data">
                 <assert_contents>
                     <has_text text="D.GPLTGTYR" />
-                    <has_n_columns n="16" />
+                    <has_n_columns n="15" />
                     <has_n_lines n="2071" />
                 </assert_contents>
             </output>
             <output name="model_qc">
                 <assert_contents>
                     <has_text text="MissingPercentage" />
-                    <has_n_columns n="15" />
+                    <has_n_columns n="13" />
                     <has_n_lines n="108" />
                 </assert_contents>
             </output>
             <output name="ResidualPlots" file="residual_plot.pdf" compare="sim_size"/>           
         </test>
 
-        <test>
+        <test expect_num_outputs="5">
             <conditional name="input">
                 <param name="input_src" value="MaxQuant"/>
                 <param name="evidence" ftype="tabular" value="test_MQ_evidence.tabular"/>
                 <param name="annotation" ftype="tabular" value="test_MQ_annotation.txt"/>
                 <param name="proteinGroups" ftype="tabular" value="test_MQ_proteingroups.tabular"/>
             </conditional>
-            <param name="selected_outputs" value="processed_data,runlevel_data"/>
+            <param name="selected_outputs" value="featurelevel_data,proteinlevel_data"/>
             <param name="selected_vis_outputs" value="ConditionPlot"/>
             <conditional name="group">
                 <param name="group_comparison" value="yes"/>
@@ -781,17 +791,18 @@
             </conditional>
             <param name="select_outputs" value="comparison_result"/>
             <param name="select_comparison_plots" value="QQPlots"/>
-            <output name="processed_data">
+            <output name="featurelevel_data">
                 <assert_contents>
                     <has_text text="SPILVATAVAAR" />
-                    <has_n_columns n="16" />
+                    <has_n_columns n="15" />
                     <has_n_lines n="61" />
                 </assert_contents>
             </output>
-            <output name="runlevel_data">
+            <output name="proteinlevel_data">
                 <assert_contents>
-                    <has_text text="qx017084.raw.thermo" />
-                    <has_n_columns n="13" />
+                    <has_text text="qx017084rawthermo" />
+                    <has_text text="sp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1" />
+                    <has_n_columns n="11" />
                     <has_n_lines n="13" />
                 </assert_contents>
             </output>
@@ -806,37 +817,38 @@
             <output name="QQPlots" file="qq_plot.pdf" compare="sim_size"/>
         </test>
         
-        <test>
+        <test expect_num_outputs="5">
             <conditional name="input">
                 <param name="input_src" value="OpenMS"/>
                 <param name="openms_input" ftype="tabular" value="openms_input.tabular"/>
             </conditional>
-            <param name="selected_outputs" value="processed_data,runlevel_data"/>
+            <param name="selected_outputs" value="featurelevel_data,proteinlevel_data"/>
             <param name="selected_vis_outputs" value="ConditionPlot"/>
             <conditional name="group">
                 <param name="group_comparison" value="yes"/>
                 <param name="comparison_matrix" ftype="tabular" value="openms_comparisonmatrix.tabular"/>
             </conditional>
             <param name="select_comparison_plots" value="Heatmap"/>
-            <output name="processed_data">
+            <output name="featurelevel_data">
                 <assert_contents>
                     <has_text text="AAAPGIQLVAGEGFQSPLEDR_2_NA_0" />
                     <has_text text="sp|P09938|RIR2_YEAST" />
-                    <has_n_columns n="16" />
+                    <has_n_columns n="15" />
                     <has_n_lines n="121" />
                 </assert_contents>
             </output>
-            <output name="runlevel_data">
+            <output name="proteinlevel_data">
                 <assert_contents>
                     <has_text text="sp|P09457|ATPO_YEAST" />
-                    <has_n_columns n="13" />
+                    <has_n_columns n="11" />
                     <has_n_lines n="76" />
                 </assert_contents>
             </output>
             <output name="ConditionPlot" file="condition_plot_openms.pdf" compare="sim_size"/>
             <output name="Heatmap" file="Heatmap_openms.pdf" compare="sim_size"/>
         </test>
-        <test>
+        
+        <test expect_num_outputs="7">
             <conditional name="input">
                 <param name="input_src" value="Skyline"/>
                 <param name="skyline_input" ftype="csv" value="skyline_input_first100.csv"/>
@@ -845,13 +857,13 @@
             </conditional>
             <conditional name="summarize">
                  <param name="MBimpute" value="FALSE"/>
-                 <param name="censoredInt" value="NULL"/>
             </conditional>
-            <param name="selected_outputs" value="log,processed_data,quant_sample_long"/>
+            <param name="censoredInt" value="NA"/>
+            <param name="selected_outputs" value="log,featurelevel_data,quant_sample_long"/>
             <param name="selected_vis_outputs" value="ProfilePlot"/>
-            <param name="featureName" value="Peptide"/>
             <param name="width" value="10"/>
             <param name="height" value="7"/>
+            <param name="featureName" value="Peptide"/>
             <conditional name="group">
                 <param name="group_comparison" value="yes"/>
                 <param name="comparison_matrix" ftype="tabular" value="comparison_matrix_skyline.tabular"/>
@@ -877,16 +889,16 @@
             </output>
             <output name="log">
                 <assert_contents>
-                    <has_text text="ADVGFLC" />
-                    <has_text text="1 level of Isotope type labeling in this experiment" />
-                    <has_text text="The required input : provided - okay" />
+                    <has_text text="3-3" />
+                    <has_text text="summaryforMultipleRows: sum" />
+                    <has_text text="Shared peptides are removed" />
                 </assert_contents>
             </output>
-             <output name="processed_data">
+             <output name="featurelevel_data">
                 <assert_contents>
-                    <has_text text="ADVGFLC[+57]NMLER_2_sum_NA" />
+                    <has_text text="ADVGFLC[+57]NMLER_2" />
                     <has_text text="319070944" />
-                    <has_n_columns n="15" />
+                    <has_n_columns n="14" />
                     <has_n_lines n="46" />
                 </assert_contents>
             </output>
@@ -894,6 +906,7 @@
                 <assert_contents>
                     <has_text text="c1-c4" />
                     <has_text text="log2FC" />
+                    <has_n_columns n="11" />
                     <has_n_lines n="4" />
                 </assert_contents>
             </output>
@@ -901,41 +914,80 @@
             <output name="VolcanoPlot" file="Volcano_plot_skyline.pdf" compare="sim_size"/>
             <output name="ComparisonPlot" file="Comparison_plot_skyline.pdf" compare="sim_size"/>
         </test>
+        
+        <test expect_num_outputs="3">
+            <conditional name="input">
+                <param name="input_src" value="Skyline"/>
+                <param name="skyline_input" ftype="csv" value="skyline_input_first100.csv"/>
+                <param name="annotation" ftype="csv" value="skyline_annotations.csv"/>
+                <param name="removeProtein_with1Peptide" value="TRUE"/>
+            </conditional>
+            <conditional name="summarize">
+                 <param name="MBimpute" value="TRUE"/>
+                 <param name="featureSubset" value="highQuality"/>
+                 <param name="remove_uninformative_feature_outlier" value="TRUE"/>
+            </conditional>
+                 <param name="censoredInt" value="0"/>
+            <param name="selected_outputs" value="log,featurelevel_data,quant_sample_matrix"/>
+            <output name="quant_sample_matrix">
+                <assert_contents>
+                    <has_text text="P32125" />
+                    <has_text text="Condition5_5" />
+                    <has_n_columns n="6" />
+                    <has_n_lines n="2" />
+                </assert_contents>
+            </output>
+            <output name="log">
+                <assert_contents>
+                    <has_text text="3-3" />
+                    <has_text text="summaryforMultipleRows: sum" />
+                    <has_text text="Shared peptides are removed" />
+                </assert_contents>
+            </output>
+             <output name="featurelevel_data">
+                <assert_contents>
+                    <has_text text="AFAEAMANNSFNADEK_2" />
+                    <has_text text="114949068" />
+                    <has_n_columns n="15" />
+                    <has_n_lines n="46" />
+                </assert_contents>
+            </output>
+        </test>
 
-        <test>
+        <test expect_num_outputs="5">
             <conditional name="input">
                 <param name="input_src" value="OpenSWATH"/>
                 <param name="openswath_input" ftype="tabular" value="test_swath_input_data.tabular"/>
                 <param name="annotation" ftype="tabular" value="test_swath_annotations.tabular"/>
             </conditional>
             <param name="selected_vis_outputs" value="QCPlot"/>
-            <output name="processed_data">
+            <output name="featurelevel_data">
                 <assert_contents>
                     <has_text text="GETLGLIGFGR" />
-                    <has_n_columns n="16" />
+                    <has_n_columns n="15" />
                     <has_n_lines n="253" />
                 </assert_contents>
             </output>
             <output name="QCPlot" file="QC_plot.pdf" compare="sim_size"/>
         </test>
 
-        <test>
+        <test expect_num_outputs="6">
             <conditional name="input">
                 <param name="input_src" value="OpenSWATH"/>
                 <param name="openswath_input" ftype="tabular" value="test_swath_input_data.tabular"/>
                 <param name="annotation" ftype="tabular" value="test_swath_annotations.tabular"/>
             </conditional>
-            <param name="selected_outputs" value="r_script,processed_data,quant_sample_long"/>
+            <param name="selected_outputs" value="r_script,featurelevel_data,quant_sample_long"/>
             <conditional name="group">
                 <param name="group_comparison" value="yes"/>
                 <param name="comparison_matrix" ftype="csv" value="test_swath_group12_comparison_matrix.csv"/>
             </conditional>
             <param name="select_outputs" value="comparison_result"/>
             <param name="select_comparison_plots" value="VolcanoPlot,ResidualPlots"/>
-            <output name="processed_data">
+            <output name="featurelevel_data">
                 <assert_contents>
                     <has_text text="GETLGLIGFGR" />
-                    <has_n_columns n="16" />
+                    <has_n_columns n="15" />
                     <has_n_lines n="253" />
                 </assert_contents>
             </output>
@@ -1079,27 +1131,14 @@
         
     - Missing value imputation: 
     
-        - Impute Missing Values: Only possible for Summarization Method TMP. Censored missing values will be determined (by censored intensity; cutoff value for censoring and Maximum quantile for deciding censored missing values") and imputed by Accelerated Failure Time model.
+        - Impute Missing Values: Only possible for Summarization Method TMP. Censored missing values will be determined and imputed by Accelerated Failure Time model.
 
         - Remove runs which have more than 50% missing values: Yes or no.
         - Censored Intensity: The processing tools report missing values differently. This option is for distinguishwhich value should be considered as missing, and further whether it is censored or at random
 
             - NA - It assumes that all NAs in Intensity column are censored.
             - 0 - It assumes that all values between 0 and 1 in Intensity column are censored. If there areNAs inIntensitywith this option, NAs will be considered as random missing.
-            - NULL - It assumes that all missing values are randomly missing.
             - Skyline and OpenSWATH input should use '0'. MaxQuant input should use 'NA'
-        - Cutoff value for censoring: cutoff for AFT model; only with censored intensity 'NA' or '0'; if NULL it assumes that there is no censored missing and any imputation will not be performed. In case that there are completely missing measurements in a run for a protein, any imputation will not be performed. In addition, the condition, which has no measurement at all in a protein, will be not impute.
-
-            - minimum value for each feature: cutoff for AFT model will be the minimum value for each feature across runs. With this option, those runs with substantial missing measurements will be biased by the cutoff value. In such case, you may remove the runs that have more than 50% missing values from the analysis.
-            - minimum value for each run: cutoff for AFT model will be the minimum value for each run across features
-            - smallest between minimum value of corresponding feature and minimum value of corresponding run: cutoff for AFT model will be the smallest value between minimum valueof corresponding feature and minimum value of corresponding run
-        - Maximum quantile for deciding censored missing values: If you don’t want to apply the threshold of noise intensity in your data, you can use maxQuantileforCensored=NULL.
-    - Missing value imputation combination with summarization method TMP:
-
-        - Summarization method: TMP + censored intensity: 'NULL': It assumes that all intensities are missing at random, therefore no action with missing value imputation: No; or error with missing value imputation: Yes.
-        - Missing value imputation: Yes + censored intensity:'NA' or '0': AFT model-based imputation using cutoff value for censoring in the AFT model
-        - Missing value imputation: No + censored intensity:'NA' or '0': censored intensities will be replaced with the value specified  in cutoff value for censoring
-        - Missing value imputation: No + censored intensity: NULL: no imputation
 
 - Group comparison: automatic detection of differentially abundant proteins between two conditions, conditions have to be specified with the 'comparison matrix'
 - Quantification per sample or group: choose the corresponding output option
@@ -1115,13 +1154,13 @@
     - MSstats log - check log file for warnings and information on the analysis steps (txt)
     - MSstats Rscript - can be used to re-run analysis outside Galaxy or to inspect the executed code (txt)
     - MSstats RawData - raw files combined into MSstats format (tabular)
-    - MSstats ProcessedData - transformed, normalized, imputed intensities (tabular)
+    - MSstats FeatureLevelData - transformed, normalized, imputed intensities (tabular)
 
         - Intensity column:  includes original intensities values
         - Abundance column:  contains the log2 transformed and normalized intensities and it will used for run-level summarization
         - Censored column:  has the decision about censored missing or not, based on censored Intensity and maximum quantile for deciding censored missing values options. Abundances with TRUE value in censored column will be considered as censored missing and imputed when Missing value imputation: Yes.
 
-    - MSstats RunlevelData - run and protein level summarized data (tabular)
+    - MSstats ProteinLevelData - run and protein level summarized data (tabular)
 
         - LogIntensities: log intensity summarized per run and protein, they will be used for the group comparison and summarized profile plot
         - NumMeasuredFeature: shows how many features were used for summarization of the corresponding run and protein
diff -r 593839e1f2c3 -r 28434abe6c5c test-data/Comparison_plot_skyline.pdf
Binary file test-data/Comparison_plot_skyline.pdf has changed
diff -r 593839e1f2c3 -r 28434abe6c5c test-data/MSstats ProfilePlot.pdf
Binary file test-data/MSstats ProfilePlot.pdf has changed
diff -r 593839e1f2c3 -r 28434abe6c5c test-data/Profile_plot_skyline.pdf
Binary file test-data/Profile_plot_skyline.pdf has changed
diff -r 593839e1f2c3 -r 28434abe6c5c test-data/Volcano_plot_skyline.pdf
Binary file test-data/Volcano_plot_skyline.pdf has changed
diff -r 593839e1f2c3 -r 28434abe6c5c test-data/featurelevel_data_skyline.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/featurelevel_data_skyline.tabular	Fri Aug 06 20:06:19 2021 +0000
@@ -0,0 +1,46 @@
+PROTEIN	PEPTIDE	TRANSITION	FEATURE	LABEL	GROUP	RUN	SUBJECT	FRACTION	originalRUN	censored	INTENSITY	ABUNDANCE	newABUNDANCE
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition1	1	1	1	121219_S_CCES_01_01_LysC_Try_1to10_Mixt_1_1raw	FALSE	319070944	29.3098413927068	29.3098413927068
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition1	1	1	1	121219_S_CCES_01_01_LysC_Try_1to10_Mixt_1_1raw	FALSE	114949068	27.8369589250684	27.8369589250684
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition1	1	1	1	121219_S_CCES_01_01_LysC_Try_1to10_Mixt_1_1raw	FALSE	132974798	28.0471170016311	28.0471170016311
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition1	2	1	1	121219_S_CCES_01_02_LysC_Try_1to10_Mixt_1_2raw	FALSE	301443168	28.0471170016311	28.0471170016311
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition1	2	1	1	121219_S_CCES_01_02_LysC_Try_1to10_Mixt_1_2raw	FALSE	864180704	29.5665639874012	29.5665639874012
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition1	2	1	1	121219_S_CCES_01_02_LysC_Try_1to10_Mixt_1_2raw	FALSE	99948868	26.4544931020782	26.4544931020782
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition1	3	1	1	121219_S_CCES_01_03_LysC_Try_1to10_Mixt_1_3raw	FALSE	275819008	28.0471170016311	28.0471170016311
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition1	3	1	1	121219_S_CCES_01_03_LysC_Try_1to10_Mixt_1_3raw	FALSE	866460512	29.6985291199933	29.6985291199933
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition1	3	1	1	121219_S_CCES_01_03_LysC_Try_1to10_Mixt_1_3raw	FALSE	104015372	26.6401918724078	26.6401918724078
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition2	4	2	1	121219_S_CCES_01_04_LysC_Try_1to10_Mixt_2_1raw	FALSE	282914080	28.0471170016311	28.0471170016311
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition2	4	2	1	121219_S_CCES_01_04_LysC_Try_1to10_Mixt_2_1raw	FALSE	887988992	29.6972948156548	29.6972948156548
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition2	4	2	1	121219_S_CCES_01_04_LysC_Try_1to10_Mixt_2_1raw	FALSE	57196342	25.7407478107147	25.7407478107147
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition2	5	2	1	121219_S_CCES_01_05_LysC_Try_1to10_Mixt_2_2raw	FALSE	306392288	28.0471170016311	28.0471170016311
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition2	5	2	1	121219_S_CCES_01_05_LysC_Try_1to10_Mixt_2_2raw	FALSE	562341792	28.9231842858172	28.9231842858172
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition2	5	2	1	121219_S_CCES_01_05_LysC_Try_1to10_Mixt_2_2raw	FALSE	61787154	25.7371158446414	25.7371158446414
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition2	6	2	1	121219_S_CCES_01_06_LysC_Try_1to10_Mixt_2_3raw	FALSE	311995872	28.0471170016311	28.0471170016311
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition2	6	2	1	121219_S_CCES_01_06_LysC_Try_1to10_Mixt_2_3raw	FALSE	947982416	29.6504503596479	29.6504503596479
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition2	6	2	1	121219_S_CCES_01_06_LysC_Try_1to10_Mixt_2_3raw	FALSE	57000615	25.5946394508612	25.5946394508612
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition3	7	3	1	121219_S_CCES_01_07_LysC_Try_1to10_Mixt_3_1raw	FALSE	317509760	28.0471170016311	28.0471170016311
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition3	7	3	1	121219_S_CCES_01_07_LysC_Try_1to10_Mixt_3_1raw	FALSE	831511536	29.4360523406791	29.4360523406791
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition3	7	3	1	121219_S_CCES_01_07_LysC_Try_1to10_Mixt_3_1raw	FALSE	110326472	26.5220950579513	26.5220950579513
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition3	8	3	1	121219_S_CCES_01_08_LysC_Try_1to10_Mixt_3_2raw	FALSE	253089648	28.0471170016311	28.0471170016311
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition3	8	3	1	121219_S_CCES_01_08_LysC_Try_1to10_Mixt_3_2raw	FALSE	909277584	29.8921892900012	29.8921892900012
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition3	8	3	1	121219_S_CCES_01_08_LysC_Try_1to10_Mixt_3_2raw	FALSE	124922268	27.0284991700692	27.0284991700692
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition3	9	3	1	121219_S_CCES_01_09_LysC_Try_1to10_Mixt_3_3raw	FALSE	330089504	28.0471170016311	28.0471170016311
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition3	9	3	1	121219_S_CCES_01_09_LysC_Try_1to10_Mixt_3_3raw	FALSE	735864592	29.2037000536836	29.2037000536836
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition3	9	3	1	121219_S_CCES_01_09_LysC_Try_1to10_Mixt_3_3raw	FALSE	54330676	25.4440986390611	25.4440986390611
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition4	10	4	1	121219_S_CCES_01_10_LysC_Try_1to10_Mixt_4_1raw	FALSE	NA	NA	NA
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition4	10	4	1	121219_S_CCES_01_10_LysC_Try_1to10_Mixt_4_1raw	FALSE	943487632	29.7700692177507	29.7700692177507
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition4	10	4	1	121219_S_CCES_01_10_LysC_Try_1to10_Mixt_4_1raw	FALSE	86579608	26.3241647855115	26.3241647855115
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition4	11	4	1	121219_S_CCES_01_11_LysC_Try_1to10_Mixt_4_2raw	FALSE	NA	NA	NA
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition4	11	4	1	121219_S_CCES_01_11_LysC_Try_1to10_Mixt_4_2raw	FALSE	600179488	29.4051505227937	29.4051505227937
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition4	11	4	1	121219_S_CCES_01_11_LysC_Try_1to10_Mixt_4_2raw	FALSE	91340524	26.6890834804686	26.6890834804686
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition4	12	4	1	121219_S_CCES_01_12_LysC_Try_1to10_Mixt_4_3raw	FALSE	NA	NA	NA
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition4	12	4	1	121219_S_CCES_01_12_LysC_Try_1to10_Mixt_4_3raw	FALSE	709016080	29.5578987363561	29.5578987363561
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition4	12	4	1	121219_S_CCES_01_12_LysC_Try_1to10_Mixt_4_3raw	FALSE	87312183	26.5363352669061	26.5363352669061
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition5	13	5	1	121219_S_CCES_01_13_LysC_Try_1to10_Mixt_5_1raw	FALSE	NA	NA	NA
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition5	13	5	1	121219_S_CCES_01_13_LysC_Try_1to10_Mixt_5_1raw	FALSE	NA	NA	NA
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition5	13	5	1	121219_S_CCES_01_13_LysC_Try_1to10_Mixt_5_1raw	FALSE	91599334	28.0471170016311	28.0471170016311
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition5	14	5	1	121219_S_CCES_01_14_LysC_Try_1to10_Mixt_5_2raw	FALSE	NA	NA	NA
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition5	14	5	1	121219_S_CCES_01_14_LysC_Try_1to10_Mixt_5_2raw	FALSE	NA	NA	NA
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition5	14	5	1	121219_S_CCES_01_14_LysC_Try_1to10_Mixt_5_2raw	FALSE	96063704	28.0471170016311	28.0471170016311
+P32125	ADVGFLC[+57]NMLER_2	NA_NA	ADVGFLC[+57]NMLER_2_NA_NA	L	Condition5	15	5	1	121219_S_CCES_01_15_LysC_Try_1to10_Mixt_5_3raw	FALSE	NA	NA	NA
+P32125	AFAEAMANNSFNADEK_2	NA_NA	AFAEAMANNSFNADEK_2_NA_NA	L	Condition5	15	5	1	121219_S_CCES_01_15_LysC_Try_1to10_Mixt_5_3raw	FALSE	836397712	29.6396138744808	29.6396138744808
+P32125	AGAAQTIVASQQR_2	NA_NA	AGAAQTIVASQQR_2_NA_NA	L	Condition5	15	5	1	121219_S_CCES_01_15_LysC_Try_1to10_Mixt_5_3raw	FALSE	91967458	26.4546201287815	26.4546201287815
diff -r 593839e1f2c3 -r 28434abe6c5c test-data/profile_wsum_plot.pdf
Binary file test-data/profile_wsum_plot.pdf has changed