# HG changeset patch
# User kpbioteam
# Date 1550841084 18000
# Node ID ab6e72fdf3509d40ad4dedb8bf25d4a5fb0a7bc0
# Parent  8a3d5d8a433f395e9da368d22ba196c8a885ed4e
Uploaded

diff -r 8a3d5d8a433f -r ab6e72fdf350 minfi_read450k.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_read450k.xml	Fri Feb 22 08:11:24 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>
+