diff mqppep_anova_script.Rmd @ 4:5c2beb4eb41c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 1c1dbc5a9838e5cd45724b6e53246eb80437e1f1

--- a/mqppep_anova_script.Rmd	Tue Jan 31 22:27:00 2023 +0000
+++ b/mqppep_anova_script.Rmd	Tue Feb 14 17:37:36 2023 +0000
@@ -81,7 +81,7 @@
   # should correlation among substrates be used (rather than covariance)
   correlateSubstrates:  TRUE
   # only show covariance among variables having variance > 1
-  filterCovVarGT1:      TRUE
+  filterCovVarGT1:      FALSE
   # maximum number of residues to display for ppeps in rownames or columnames
   ppepTruncN:           10
   # maximum number of characters of subgenes to display in rownames or columnames
@@ -97,9 +97,6 @@
   kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2"
   # should debugging trace messages be printed?
   showEnrichedSubstrates: FALSE
-  # should debugging nb/nbe messages be printed?
-  printNBMsgs:          FALSE
-  #printNBMsgs:          TRUE
   # should row-scaling be applied to heatmaps: "none" or "row"
   defaultHeatMapRowScaling: !r c("none", "row")[1]
   # how missing values be displayed on heat maps: "NA" or " "
@@ -115,6 +112,9 @@
   # when debugging files are needed, set debugFileBasePath to the path
   #   to the directory where they should be written
   debugFileBasePath:    !r if (TRUE) NULL else "test-data"
+  # should debugging nb/nbe messages be printed?
+  printNBMsgs:          FALSE
+  #printNBMsgs:          TRUE
 ---
 
 ```{r setup, include = FALSE, results = 'asis'}
@@ -6011,7 +6011,7 @@
            p_value_data
          WHERE ppep = phosphopeptide
          GROUP BY kinase, ppep
-         ORDER BY kinase, ppep, p_value_data.quality DESC
+         ORDER BY kinase, p_value_data.quality DESC
       "),
       justification = "l l l l l l l",
       centered = TRUE,