| Previous changeset 0:80b40b9ab835 (2020-07-25) Next changeset 2:52ac6fde9a5b (2020-08-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" |
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modified:
msstats.xml |
| b |
| diff -r 80b40b9ab835 -r 3e2606fa85bf msstats.xml --- 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"> |