Mercurial > repos > davidecangelosi > pipe_t

changeset 27:5618ea415c4a draft

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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 157954c8b7e2c009e0e40a3a7e19ede7cab0de9e
author davidecangelosi
date Fri, 31 May 2019 10:25:13 -0400
parents f008adc272a2
children 7fbfe6f424f0
files pipe-t.R pipe-t.xml
diffstat 2 files changed, 0 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/pipe-t.R	Fri May 31 08:09:25 2019 -0400
+++ b/pipe-t.R	Fri May 31 10:25:13 2019 -0400
@@ -25,7 +25,6 @@
 library(affy)
 library(psych)
 library(zoo)
-library(Hmisc)
 })
 
 cat("\n R libraries...loaded!\n")
@@ -853,12 +852,6 @@
     "cubic"={
      exprs(qFiltNAs) <- na.spline(exprs(qFiltNAs))
     },
-    "mean"={
-      exprs(qFiltNAs)<-impute(exprs(qFiltNAs),mean)
-    },
-    "median"={
-      exprs(qFiltNAs)<-impute(exprs(qFiltNAs),median)
-    },
     stop("Enter something that switches me!")
 )
 
--- a/pipe-t.xml	Fri May 31 08:09:25 2019 -0400
+++ b/pipe-t.xml	Fri May 31 10:25:13 2019 -0400
@@ -10,7 +10,6 @@
 <requirement type="package" version="1.11.0">r-bbmisc</requirement>
 <requirement type="package" version="1.8.4">r-psych</requirement>
 <requirement type="package" version="1.8_3">r-zoo</requirement>
-<requirement type="package" version="4.1_1">r-hmisc</requirement>
 <requirement type="package" version="1.28.0">bioconductor-normqpcr </requirement>
 </requirements>
 <stdio>
@@ -214,8 +213,6 @@
     <param name="format" type="select"  label="Select one of the imputation methods from the list below." help="">
       <option value="mestdagh" selected="true">Mestdagh</option>
       <option value="knn">K-Nearest Neighbour</option>
-      <option value="mean">Mean</option>
-      <option value="median">Median</option>
       <option value="cubic">Cubic Spline</option>
     </param>
     <when value="knn">