| Previous changeset 3:dda27b9273a8 (2023-01-31) Next changeset 5:514afed1f40d (2023-02-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 1c1dbc5a9838e5cd45724b6e53246eb80437e1f1 |
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modified:
macros.xml mqppep_anova_script.Rmd |
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| diff -r dda27b9273a8 -r 2d9f216c1048 macros.xml --- a/macros.xml Tue Jan 31 22:27:14 2023 +0000 +++ b/macros.xml Tue Feb 14 17:37:48 2023 +0000 |
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| @@ -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> |
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| diff -r dda27b9273a8 -r 2d9f216c1048 mqppep_anova_script.Rmd --- a/mqppep_anova_script.Rmd Tue Jan 31 22:27:14 2023 +0000 +++ b/mqppep_anova_script.Rmd Tue Feb 14 17:37:48 2023 +0000 |
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| @@ -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, |