# HG changeset patch
# User eschen42
# Date 1666908698 0
# Node ID 42b207aaa527af70f902255e11d385f2f0404164
# Parent  896eb8ae1c8c583b27f2901a925061fc714d328b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 83864e12abbf63728a389b7fe677f3b88844e03f

diff -r 896eb8ae1c8c -r 42b207aaa527 mqppep_anova_script.Rmd
--- a/mqppep_anova_script.Rmd	Thu Oct 27 19:48:51 2022 +0000
+++ b/mqppep_anova_script.Rmd	Thu Oct 27 22:11:38 2022 +0000
@@ -106,171 +106,7 @@
   #   to the directory where they should be writtn
   debugFileBasePath:    !r if (TRUE) NULL else "test-data"
 ---
-<!--
-  alphaFile:            "test-data/alpha_levels.tabular"
-  inputFile:            "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
-  preprocDb:            "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
-  kseaAppPrepDb:        !r c(":memory:", "test-data/mqppep.sqlite")[2]
-  regexSampleNames:     "\\.\\w+\\.\\d+[A-Z]$"
-  regexSampleGrouping:  "\\w+"
-  groupFilterPatterns:  ".+"
-  groupFilter:    !r c("none", "exclude", "include")[3]
-  imputationMethod:     !r c("group-median", "median", "mean", "random")[1]
-  kseaCutoffThreshold:  !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[1]
-  ut_alphaFile:            "test-data/alpha_levels.tabular"
-  ut_inputFile:            "test-data/UT_phospho_ST_sites.preproc.tabular"
-  ut_preprocDb:            "test-data/UT_phospho_ST_sites.preproc.sqlite"
-  ut_kseaAppPrepDb:        !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
-  ut_regexSampleNames:     "\\.\\d+[A-Z]$"
-  ut_regexSampleGrouping:  "\\d+"
-  ut_groupFilterPatterns:  ".+,.*"
-  ut_groupFilter:    !r c("none", "exclude", "include")[1]
-  ut_imputationMethod:     !r c("group-median", "median", "mean", "random")[4]
-  ut_kseaCutoffThreshold:  !r c(0.05, 0.1, 0.25, 0.5, 0.9)[1]
-  tst_alphaFile:            "test-data/alpha_levels.tabular"
-  tst_inputFile:            "test-data/test_input_for_anova.tabular"
-  tst_preprocDb:            "test-data/test_input_for_anova.sqlite"
-  tst_kseaAppPrepDb:        !r c(":memory:", "test-data/mqppep.sqlite")[2]
-  tst_regexSampleNames:     "\\.\\d+[A-Z]$"
-  tst_regexSampleGrouping:  "\\d+"
-  tst_groupFilterPatterns:  ".+"
-  tst_groupFilter:    !r c("none", "exclude", "include")[1]
-  tst_imputationMethod:     !r c("group-median", "median", "mean", "random")[4]
-  tst_kseaCutoffThreshold:  !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5]
-
-  tst_alphaFile:            "test-data/alpha_levels.tabular"
-  tst_inputFile:            "test-data/UT_phospho_ST_sites.preproc.tabular"
-  tst_preprocDb:            "test-data/UT_phospho_ST_sites.preproc.sqlite"
-  tst_kseaAppPrepDb:        !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
-  tst_regexSampleNames:     "\\.\\d+[A-Z]$"
-  tst_regexSampleGrouping:  "\\d+"
-  tst_groupFilterPatterns:  ".+,.*"
-  tst_groupFilter:    !r c("none", "exclude", "include")[1]
-  tst_imputationMethod:     !r c("group-median", "median", "mean", "random")[4]
-  tst_kseaCutoffThreshold:  !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[5]
-  px_alphaFile:            "test-data/alpha_levels.tabular"
-  px_inputFile:            "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
-  px_preprocDb:            "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
-  px_kseaAppPrepDb:        !r c(":memory:", "test-data/mqppep.sqlite")[2]
-  px_regexSampleNames:     "\\.\\w+\\.\\d+[A-Z]$"
-  px_regexSampleGrouping:  "\\w+"
-  px_groupFilterPatterns:  ".+"
-  px_groupFilter:    !r c("none", "exclude", "include")[3]
-  px_imputationMethod:     !r c("group-median", "median", "mean", "random")[4]
-  px_kseaCutoffThreshold:  !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[5]
-  pdx_alphaFile:            "test-data/alpha_levels.tabular"
-  pdx_inputFile:            "test-data/PDX012970_pST.preproc_tab.tabular"
-  pdx_preprocDb:            "test-data/PDX012970_pST.preproc.sqlite"
-  pdx_kseaAppPrepDb:        !r c(":memory:", "test-data/PDX012970.sqlite")[2]
-  pdx_regexSampleNames:     "\\.\\w+\\.\\w+\\.\\d+[A-Z]$"
-  pdx_regexSampleGrouping:  "\\.\\w+\\K\\.\\w+"
-  pdx_groupFilterPatterns:  "AdCa,AVPC"
-  pdx_groupFilter:    !r c("none", "exclude", "include")[3]
-  pdx_imputationMethod:     !r c("group-median", "median", "mean", "random")[4]
-  pdx_kseaCutoffThreshold:  !r c(0.05, 0.1, 0.25, 0.5, 0.9)[1]
-  tst_alphaFile:            "test-data/alpha_levels.tabular"
-  tst_inputFile:            "test-data/test_input_for_anova.tabular"
-  tst_preprocDb:            "test-data/test_input_for_anova.sqlite"
-  tst_kseaAppPrepDb:        !r c(":memory:", "test-data/mqppep.sqlite")[2]
-  tst_regexSampleNames:     "\\.\\d+[A-Z]$"
-  tst_regexSampleGrouping:  "\\d+"
-  tst_groupFilterPatterns:  ".+"
-  tst_groupFilter:    !r c("none", "exclude", "include")[1]
-  tst_kseaCutoffThreshold:  !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5]
-  tst_imputationMethod:     !r c("group-median", "median", "mean", "random")[1]
-  ut_alphaFile:            "test-data/alpha_levels.tabular"
-  ut_inputFile:            "test-data/UT_phospho_ST_sites.preproc.tabular"
-  ut_preprocDb:            "test-data/UT_phospho_ST_sites.preproc.sqlite"
-  ut_kseaAppPrepDb:        !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
-  ut_regexSampleNames:     "\\.\\d+[A-Z]$"
-  ut_regexSampleGrouping:  "\\d+"
-  ut_groupFilterPatterns:  ".+,.*"
-  ut_groupFilter:    !r c("none", "exclude", "include")[1]
-  ut_imputationMethod:     !r c("group-median", "median", "mean", "random")[4]
-  alphaFile:            "test-data/alpha_levels.tabular"
-  inputFile:            "test-data/test_input_for_anova.tabular"
-  preprocDb:            "test-data/test_input_for_anova.sqlite"
-  kseaAppPrepDb:        !r c(":memory:", "test-data/mqppep.sqlite")[2]
-  regexSampleNames:     "\\.\\d+[A-Z]$"
-  regexSampleGrouping:  "\\d+"
-  groupFilterPatterns:  ".+,.*"
-  groupFilter:    !r c("none", "exclude", "include")[1]
-  imputationMethod:     !r c("group-median", "median", "mean", "random")[4]
-  nd_alphaFile:            "test-data/alpha_levels.tabular"
-  nd_inputFile:            "test-data/pST_Sites_NancyDu.txt.preproc.tabular"
-  nd_preprocDb:            "test-data/pST_Sites_NancyDu.txt.preproc.sqlite"
-  nd_kseaAppPrepDb:        !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]
-  nd_regexSampleNames:     "\\.\\d+[A-Z]$"
-  nd_regexSampleGrouping:  "\\d+"
-  nd_groupFilterPatterns:     ".+,.*"
-  nd_groupFilter:    !r c("none", "exclude", "include")[1]
-  nd_imputationMethod:     !r c("group-median", "median", "mean", "random")[4]
-  pxd_alphaFile:            "test-data/alpha_levels.tabular"
-  pxd_inputFile:            "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
-  pxd_preprocDb:            "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
-  pxd_kseaAppPrepDb:        !r c(":memory:", "test-data/mqppep.sqlite")[2]
-  pxd_regexSampleNames:     "\\.\\w+\\.\\d+[A-Z]$"
-  pxd_regexSampleGrouping:  "\\w+"
-  pxd_groupFilterPatterns:     ".+"
-  pxd_groupFilter:    !r c("none", "exclude", "include")[3]
-  pxd_imputationMethod:     !r c("group-median", "median", "mean", "random")[4]
-
-  alphaFile:            "test-data/alpha_levels.tabular"
-  inputFile:            "test-data/test_input_for_anova.tabular"
-  preprocDb:            "test-data/test_input_for_anova.sqlite"
-  kseaAppPrepDb:        !r c(":memory:", "test-data/mqppep.sqlite")[2]
-  regexSampleNames:     "\\.\\d+[A-Z]$"
-  regexSampleGrouping:  "\\d+"
-  groupFilterPatterns:  ".+,.*"
-  groupFilter:    !r c("none", "exclude", "include")[1]
-
-  alphaFile:            "test-data/alpha_levels.tabular"
-  inputFile:            "test-data/PDX012970_pST.preproc_tab.tabular"
-  preprocDb:            "test-data/PDX012970_pST.preproc.sqlite"
-  kseaAppPrepDb:        !r c(":memory:", "test-data/PDX012970.sqlite")[2]
-  regexSampleNames:     "\\.\\w+\\.\\w+\\.\\d+[A-Z]$"
-  regexSampleGrouping:  "\\.\\w+\\K\\.\\w+"
-  groupFilterPatterns:  "AdCa,AVPC"
-  groupFilter:    !r c("none", "exclude", "include")[3]
-
-  alphaFile:            "test-data/alpha_levels.tabular"
-  inputFile:            "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
-  preprocDb:            "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
-  kseaAppPrepDb:        !r c(":memory:", "test-data/mqppep.sqlite")[2]
-  regexSampleNames:     "\\.\\w+\\.\\d+[A-Z]$"
-  regexSampleGrouping:  "\\w+"
-  groupFilterPatterns:     ".+,.*"
-  groupFilter:    !r c("none", "exclude", "include")[3]
-
-  kseaCutoffStatistic:  !r c("p.value", "FDR")[2]
-  kseaCutoffThreshold:  !r c(0.05, 0.1)[1]
-
-  alphaFile:            "test-data/alpha_levels.tabular"
-  inputFile:            "test-data/UT_phospho_ST_sites.preproc.tabular"
-  preprocDb:            "test-data/UT_phospho_ST_sites.preproc.sqlite"
-  kseaAppPrepDb:        !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
-  regexSampleNames:     "\\.\\d+[A-Z]$"
-  regexSampleGrouping:  "\\d+"
-
-  alphaFile:            "test-data/alpha_levels.tabular"
-  inputFile:            "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.tabular"
-  preprocDb:            "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.sqlite"
-  kseaAppPrepDb:        !r c(":memory:", "test-data/pY_Sites_NancyDu.ksea.sqlite")[2]
-  regexSampleNames:     "\\.\\d+[A-Z]$"
-  regexSampleGrouping:  "\\d+"
-  groupFilterPatterns:  ".+,.*"
-  groupFilter:    !r c("none", "exclude", "include")[3]
-
-  alphaFile:            "test-data/alpha_levels.tabular"
-  inputFile:            "test-data/pST_Sites_NancyDu.txt.preproc.tabular"
-  preprocDb:            "test-data/pST_Sites_NancyDu.txt.preproc.sqlite"
-  kseaAppPrepDb:        !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]
-  regexSampleNames:     "\\.\\d+[A-Z]$"
-  regexSampleGrouping:  "\\d+"
-  groupFilterPatterns:  ".+,.*"
-  groupFilter:    !r c("none", "exclude", "include")[1]
-
--->
+
 ```{r setup, include = FALSE, results = 'asis'}
 
 # simple debug messaging