Mercurial > repos > galaxyp > mqppep_preproc

changeset 4:5c2beb4eb41c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 1c1dbc5a9838e5cd45724b6e53246eb80437e1f1
author galaxyp
date Tue, 14 Feb 2023 17:37:36 +0000
parents bae3a23461c9
children b889e05ce77d
files macros.xml mqppep_anova_script.Rmd
diffstat 2 files changed, 6 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Jan 31 22:27:00 2023 +0000
+++ b/macros.xml	Tue Feb 14 17:37:36 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.1.17</token>
+    <token name="@TOOL_VERSION@">0.1.18</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
@@ -22,10 +22,6 @@
             <requirement type="package" version="1.7.3"   >r-optparse</requirement>
             <requirement type="package" version="1.4.4"   >r-reshape2</requirement>
             <requirement type="package" version="2.17"    >r-rmarkdown</requirement>
-            <!--
-            <requirement type="package" version="2.2.18"  >r-rsqlite</requirement>
-            <requirement type="package" version="0.4.2"   >r-sass</requirement>
-            -->
             <requirement type="package" version="1.2.2"   >r-sessioninfo</requirement>
             <requirement type="package" version="0.4_11"  >r-sqldf</requirement>
             <requirement type="package" version="1.4.1"   >r-stringr</requirement>
--- 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,