# HG changeset patch
# User galaxyp
# Date 1582673028 18000
# Node ID 2bc6bbf651b95e12c016724d53e47d519af2e15c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
diff -r 000000000000 -r 2bc6bbf651b9 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Feb 25 18:23:48 2020 -0500
@@ -0,0 +1,23 @@
+
+ 2.1.4
+
+
+
+ pyprophet
+
+
+
+
+
+
+ 10.1038/nmeth.4398
+ 10.1038/nbt.3908
+ 10.1093/bioinformatics/btu686
+ 10.1038/nmeth.1584
+
+
+
+
+ http://openswath.org/en/latest/docs/pyprophet.html
+
+
diff -r 000000000000 -r 2bc6bbf651b9 pyprophet_export.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pyprophet_export.xml Tue Feb 25 18:23:48 2020 -0500
@@ -0,0 +1,364 @@
+
+
+ Export tabular files, optional swath2stats export
+
+
+ macros.xml
+
+
+ bioconductor-swath2stats
+ r-dplyr
+ r-data.table
+ r-gridextra
+
+
+
+
+
+ % group_by(ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, BioReplicate, Condition, Run) %>% summarise(Intensity = sum(Intensity))
+
+Test = Test[, c("ProteinName", "PeptideSequence", "PrecursorCharge", "FragmentIon", "ProductCharge", "IsotopeLabelType", "Intensity", "BioReplicate", "Condition", "Run")]
+
+write.table(Test, file="$msstats_input", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
+write.table(peptide_signal, file="$peptide_signal", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
+write.table(protein_signal, file="$protein_signal", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
+
+#end if
+
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ conditional_output['format'] != 'score_plots'
+
+
+ conditional_output['format'] == 'score_plots'
+
+
+ conditional_swath2stats['swath2stats'] == 'yes_swath2stats'
+
+
+ conditional_swath2stats['swath2stats'] == 'yes_swath2stats'
+
+
+ conditional_swath2stats['swath2stats'] == 'yes_swath2stats'
+
+
+ conditional_swath2stats['swath2stats'] == 'yes_swath2stats'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1371/journal.pone.0153160
+
+
diff -r 000000000000 -r 2bc6bbf651b9 test-data/merged.osw
Binary file test-data/merged.osw has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/open_swath_output1.osw
Binary file test-data/open_swath_output1.osw has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/open_swath_output2.osw
Binary file test-data/open_swath_output2.osw has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tabular Tue Feb 25 18:23:48 2020 -0500
@@ -0,0 +1,1 @@
+transition_group_id decoy run_id filename RT assay_rt delta_rt iRT assay_iRT delta_iRT Sequence FullPeptideName Charge mz Intensity aggr_prec_Peak_Area aggr_prec_Peak_Apex leftWidth rightWidth peak_group_rank d_score m_score id aggr_Peak_Area aggr_Peak_Apex aggr_Fragment_Annotation ProteinName m_score_peptide_experiment_wide m_score_peptide_global m_score_protein_experiment_wide m_score_protein_global
diff -r 000000000000 -r 2bc6bbf651b9 test-data/patient_specific_OSW_optimized_decoys.pqp
Binary file test-data/patient_specific_OSW_optimized_decoys.pqp has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/peptide1.osw
Binary file test-data/peptide1.osw has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/peptide1.pdf
Binary file test-data/peptide1.pdf has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/peptide2.osw
Binary file test-data/peptide2.osw has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/peptide2.pdf
Binary file test-data/peptide2.pdf has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/protein1.osw
Binary file test-data/protein1.osw has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/protein1.pdf
Binary file test-data/protein1.pdf has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/protein2.osw
Binary file test-data/protein2.osw has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/protein2.pdf
Binary file test-data/protein2.pdf has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/score.osw
Binary file test-data/score.osw has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/score_plots.pdf
Binary file test-data/score_plots.pdf has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/score_report.pdf
Binary file test-data/score_report.pdf has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/study_design.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/study_design.tabular Tue Feb 25 18:23:48 2020 -0500
@@ -0,0 +1,3 @@
+Filename Condition BioReplicate Run
+./TN22.mzML late 1 1
+./TN23.mzML early 2 2
diff -r 000000000000 -r 2bc6bbf651b9 test-data/subsample.tabular
Binary file test-data/subsample.tabular has changed
diff -r 000000000000 -r 2bc6bbf651b9 test-data/test_data.osw
Binary file test-data/test_data.osw has changed