changeset 1:3e2606fa85bf draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79"

--- a/msstats.xml	Sat Jul 25 13:21:47 2020 -0400
+++ b/msstats.xml	Sat Jul 25 14:49:56 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="msstats" name="MSstats" version="@VERSION@.0" python_template_version="3.5">
+<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@">3.20.1</token>
@@ -27,9 +27,8 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         cat '$msstats_script' > '$r_script' &&
-        cat '$msstats_script' &&
         Rscript '$msstats_script'
-        && cat msstats*.log > $log
+        && cat msstats*.log > '$log'
     ]]></command>
     <configfiles>
         <configfile name="msstats_script"><![CDATA[
@@ -217,9 +216,6 @@
 write.table(comparisons\$ModelQC, "ModelQC.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
   #end if
 
-## TODO: transform fittedmodel to table 
-##class(DDA2009.comparisons$fittedmodel) # list, probably good to output this somehow
-
 ## Visualizations:
 
   #if 'qqplot' in $group.select_outputs
@@ -262,7 +258,9 @@
             <param name="input_src" type="select" label="input source">
                 <option value="MSstats">MStats 10 column format</option>
                 <option value="MaxQuant">MaxQuant</option>
+                <!-- 
                 <option value="OpenMS">OpenMS</option>
+                -->
                 <option value="OpenSWATH">OpenSWATH</option>
             </param>
             <when value="MSstats">
@@ -285,6 +283,7 @@
                     <expand macro="removeProtein_with1Peptide"/>
                 </section>
             </when>
+            <!--
             <when value="OpenMS">
                 <param name="evidence" type="data" format="tabular,csv" label="OpenSWATH_input"/>
                 <param name="annotation" type="data" format="tabular,csv" label="OpenSWATH_annotation"/>
@@ -295,6 +294,7 @@
                     <expand macro="removeProtein_with1Peptide"/>
                 </section>
             </when>
+            -->
             <when value="OpenSWATH">
                 <param name="evidence" type="data" format="tabular,csv" label="OpenSWATH_input"/>
                 <param name="annotation" type="data" format="tabular,csv" label="OpenSWATH_annotation"/>
@@ -421,9 +421,15 @@
         </data>
         <data name="processed_data" format="tabular" label="MSstats ProcessedData" from_work_dir="ProcessedData.tsv">
             <filter>'processed_data' in 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="MSstats RunlevelData" from_work_dir="RunlevelData.tsv">
             <filter>'runlevel_data' in 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>
         </data>
         <data name="qcplot" format="pdf" label="MSstats QCPlot.pdf" from_work_dir="MSStats_only_QCPlot.pdf">
             <filter>'qcplot' in selected_outputs</filter>
@@ -442,21 +448,33 @@
         </data>
         <data name="quant_sample_long" format="tabular" label="MSstats SampleQuantificationLong.tsv" from_work_dir="SampleQuantificationLong.tsv">
             <filter>'quant_sample_long' in selected_outputs</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Protein,Group_Subject,LogIntensity" />
+            </actions>
         </data>
         <data name="quant_group_matrix" format="tabular" label="MSstats GroupQuantificationMatrix.tsv" from_work_dir="GroupQuantificationMatrix.tsv">
             <filter>'quant_group_matrix' in selected_outputs</filter>
         </data>
         <data name="quant_group_long" format="tabular" label="MSstats GroupQuantificationLong.tsv" from_work_dir="GroupQuantificationLong.tsv">
             <filter>'quant_group_long' in selected_outputs</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Protein,Group,LogIntensity" />
+            </actions>
         </data>
         <data name="comparison_result" format="tabular" label="MSstats ComparisonResult.tsv" from_work_dir="ComparisonResult.tsv">
             <filter> group['group_comparison'] == 'yes' and 'comparison_result' in group['select_outputs']</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Protein,Label,log2FC,SE,Tvalue,DF,pvalue,adj.pvalue,issue,MissingPercentage,ImputationPercentage" />
+            </actions>
         </data>
         <data name="fittedmodel" format="txt" label="MSstats ComparisonFittedModel.txt" from_work_dir="ComparisonFittedModel.txt">
             <filter> group['group_comparison'] == 'yes' and 'fittedmodel' in group['select_outputs']</filter>
         </data>
         <data name="model_qc" format="tabular" label="MSstats ModelQC.tsv" from_work_dir="ModelQC.tsv">
             <filter> group['group_comparison'] == 'yes' and 'model_qc' in group['select_outputs']</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="RUN,PROTEIN,ABUNDANCE,NumMeasuredFeature,MissingPercentage,more50missing,NumImputedFeature,originalRUN,GROUP,GROUP_ORIGINAL,SUBJECT_ORIGINAL,SUBJECT_NESTED,SUBJECT,residuals,fitted" />
+            </actions>
         </data>
         <data name="qqplot" format="pdf" label="MSstats ModelQQ.pdf" from_work_dir="MSStats_group_QQPlot.pdf">
             <filter> group['group_comparison'] == 'yes' and 'qqplot' in group['select_outputs']</filter>
@@ -473,9 +491,6 @@
         <data name="comparisonplot" format="pdf" label="MSstats ComparisonPlot.pdf" from_work_dir="MSStats_group_ComparisonPlot.pdf">
             <filter> group['group_comparison'] == 'yes' and 'comparisonplot' in group['select_outputs']</filter>
         </data>
-<!--
-Tabular file (from groupcomparison): "fittedmodel"
--->
     </outputs>
     <tests>
 
@@ -575,9 +590,6 @@
             <output name="qqplot" file="qq_plot.pdf" compare="sim_size"/>                     
         </test>
         
-        
-                          
-
         <!--
         <test>
             <conditional name="input">