# HG changeset patch
# User kpbioteam
# Date 1550851803 18000
# Node ID 0d296a6a18d3dd727af270b7d6379573116af05a
# Parent  07a4b49cd165eac58db63cabdff43e9affed49bf
Uploaded

diff -r 07a4b49cd165 -r 0d296a6a18d3 minfi_read450k.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_read450k.xml	Fri Feb 22 11:10:03 2019 -0500
@@ -0,0 +1,46 @@
+<tool id="minfi_read450k" name="minfi_read450k" version="2.1.0">
+  <description>load .IDAT files</description>
+  <requirements>
+  <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+      #for $counter, $file in enumerate($files_red):
+      ln -s $file ./${counter+1}_Red.idat &&
+        #end for
+        #for $counter, $file in enumerate($files_grn):
+        ln -s $file ./${counter+1}_Grn.idat &&
+        #end for
+        Rscript '$read_idat_script'
+      ]]></command>
+      <configfiles>
+      <configfile name="read_idat_script"><![CDATA[
+        require("minfi", quietly = TRUE)
+        files<-list()
+        #for $counter, $input in enumerate($files_red):
+        files['${counter+1}'] <- '${counter+1}'
+        #end for
+        out <- read.metharray(files)
+        save(out, file = '$RGChannelSet')
+        ]]> </configfile>
+        </configfiles>
+        <inputs>
+        <param type="data" name="files_red" multiple="true" format="idat" label="Red .IDAT files"/>
+          <param type="data" name="files_grn" multiple="true" format="idat" label="Green .IDAT files" />
+            </inputs>
+            <outputs>
+            <data name="RGChannelSet" format="rdata" label="RGChannelSet"/>
+              </outputs>
+             <tests>
+        <test>
+            <param name="files_red" value="GSM1588707_8795207119_R06C02_Red.idat,GSM1588706_8795207135_R02C02_Red.idat,GSM1588705_8795207119_R05C02_Red.idat,GSM1588704_8795207135_R01C02_Red.idat" ftype="idat"/>
+            <param name="files_grn" value="GSM1588707_8795207119_R06C02_Grn.idat,GSM1588706_8795207135_R02C02_Grn.idat,SM1588705_8795207119_R05C02_Grn.idat,GSM1588704_8795207135_R01C02_Grn.idat" ftype="idat"/>
+            <output name="RGChannelSet" file="RGChannelSet.rdata"/>
+        </test>
+    </tests>
+                    <help><![CDATA[
+                      The tool load the binary 450K array “IDAT” raw files generated by the Illumina Scanner. In addition to the methylated and an unmethylated intensity values for each 450,000 CpG positions, IDAT file contains some extra info such as control probes.]]></help>
+                    <citations>
+                    <citation type="doi">10.18129/B9.bioc.illuminaio</citation>
+                      </citations>
+                      </tool>
+