# HG changeset patch
# User kpbioteam
# Date 1528821086 14400
# Node ID a9bdbb07134601ee3d9e57eafaba11afd77de8fa
# Parent  3d15f8823c986eb14044dec9a4f88f51bd0aa2a0
planemo upload for repository https://github.com/kpbioteam/minfi_dmr commit 65d01f00526cadfcd1f52d06243fbc87ffee462f-dirty

diff -r 3d15f8823c98 -r a9bdbb071346 minfi_dmr.R
--- a/minfi_dmr.R	Tue Jun 12 12:10:56 2018 -0400
+++ b/minfi_dmr.R	Tue Jun 12 12:31:26 2018 -0400
@@ -1,5 +1,4 @@
 require("minfi", quietly = TRUE)
-require("rtracklayer", quietly = TRUE)
 
 options(warn = -1)
 options("download.file.method"="wget")
@@ -16,8 +15,7 @@
 input7 = args[7]
 input8 = args[8]
 input9 = args[9]
-input10 =args[10]
-output1 = args[11]
+output1 = args[10]
 
 GRSet <- get(load(input1))
 
@@ -47,7 +45,6 @@
 nullMethod <- input8
 coef <- 2 #default
 verbose <- input9
-meth <- as.numeric(input10)
 
 dmrs <- bumphunter(GRSet,
                     design = design.matrix, 
@@ -60,6 +57,5 @@
 
 
 dmrGR <- with(dmrs$table,GRanges(chr,IRanges(start,end),area=area,value=value))
-dmrGR$type <- ifelse(abs(dmrGR$value)<meth, "neither", ifelse(dmrGR$value<0,"hypo","hyper"))
 
 write.table(dmrGR, file= output1, quote = FALSE, row.names = FALSE, sep = "\t")
diff -r 3d15f8823c98 -r a9bdbb071346 minfi_dmr.xml
--- a/minfi_dmr.xml	Tue Jun 12 12:10:56 2018 -0400
+++ b/minfi_dmr.xml	Tue Jun 12 12:31:26 2018 -0400
@@ -4,7 +4,7 @@
         <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
 </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        Rscript  ${__tool_directory__}/minfi_dmr.R "$input1" "$input2" "$input3" "$input4" "$input5" "$input6" "$input7" "$input8" "$input9""$input10" "$output1"
+        Rscript  ${__tool_directory__}/minfi_dmr.R "$input1" "$input2" "$input3" "$input4" "$input5" "$input6" "$input7" "$input8" "$input9" "$output1"
     ]]></command>
     <inputs>
         <param type="data" name="input1" format="rdata" label="Genomic Ratio Set" />
@@ -23,7 +23,6 @@
                         <option value="TRUE">TRUE</option>
                         <option value="FALSE">FALSE</option>
                     </param>
-     <param name="input10" type="text" value="0.2" label="Set up Difference" help="Set up difference for an annotation hypo- or hyper- methylation"/>
  </inputs>
     <outputs>
         <data name="output1" format="bed" label="Differentially Methylated Regions" /> 
@@ -39,7 +38,6 @@
             <param name="input7" value="0.02"/>
             <param name="input8" value="permutation"/>
             <param name="input9" value="FALSE"/>
-            <param name="input10" value="0.2"/>
             <output name="output1" file="dmr.bed"/>
         </test>
     </tests>