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changeset 76:fef50103f6b3 draft

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planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
author kpbioteam
date Fri, 07 Jun 2019 08:57:26 -0400
parents 9c6fbb7d5a2a
children c7e8fdb9f1db
files minfi_read450k.xml
diffstat 1 files changed, 9 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/minfi_read450k.xml	Mon May 20 07:14:26 2019 -0400
+++ b/minfi_read450k.xml	Fri Jun 07 08:57:26 2019 -0400
@@ -4,22 +4,20 @@
         <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 &&
+      #for $counter, $input in enumerate($files_red):
+        #set $redname = str( getattr( $input, 'element_identifier', 'sample' ) ).replace( "/", '-' ).replace( "\t", "-" )
+        ln -s $input ./${redname} &&
       #end for
-      #for $counter, $file in enumerate($files_grn):
-            ln -s $file ./${counter+1}_Grn.idat &&
+      #for $counter, $input in enumerate($files_grn):
+        #set $grnname = str( getattr( $input, 'element_identifier', 'sample' ) ).replace( "/", '-' ).replace( "\t", "-" )
+        ln -s $input ./${grnname} &&
       #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)
+        out <- read.metharray(list.files(pattern="_Red.idat"))
         save(out, file = '$RGChannelSet')
         ]]> </configfile>
         </configfiles>
@@ -33,12 +31,12 @@
              <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"/>
+            <param name="files_grn" value="GSM1588707_8795207119_R06C02_Grn.idat,GSM1588706_8795207135_R02C02_Grn.idat,GSM1588705_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.
+The tool loads 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>