# HG changeset patch
# User galaxyp
# Date 1615557768 0
# Node ID 5909bdc01143be421783f5f1e6e924ac534ac271
# Parent  adce265c7051e7afffa2bbd0d0ed195adeb5842c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa"

diff -r adce265c7051 -r 5909bdc01143 msstatstmt.xml
--- a/msstatstmt.xml	Sat Feb 27 10:53:56 2021 +0000
+++ b/msstatstmt.xml	Fri Mar 12 14:02:48 2021 +0000
@@ -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.
diff -r adce265c7051 -r 5909bdc01143 test-data/MSstats_group_ComparisonPlot.pdf
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diff -r adce265c7051 -r 5909bdc01143 test-data/MSstats_group_Heatmap.pdf
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diff -r adce265c7051 -r 5909bdc01143 test-data/MSstats_group_VolcanoPlot.pdf
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diff -r adce265c7051 -r 5909bdc01143 test-data/ProfilePlot.pdf
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diff -r adce265c7051 -r 5909bdc01143 test-data/ProfilePlot_allonly.pdf
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diff -r adce265c7051 -r 5909bdc01143 test-data/ProfilePlot_list.pdf
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diff -r adce265c7051 -r 5909bdc01143 test-data/QCPlot.pdf
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