# HG changeset patch
# User kpbioteam
# Date 1558350866 14400
# Node ID 9c6fbb7d5a2a7b501f3a3403ed2470553bafb518
# Parent  53aaf097238cbcc33e49f4c18bad76a384e3c0ee
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty

diff -r 53aaf097238c -r 9c6fbb7d5a2a macros.xml
--- a/macros.xml	Thu May 16 08:56:35 2019 -0400
+++ b/macros.xml	Mon May 20 07:14:26 2019 -0400
@@ -1,11 +1,11 @@
 <macros>
-<token name="@VERSION@">1.28.0</token>
+    <token name="@VERSION@">@MINFI_VERSION@</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="3.5.1">r-base</requirement>
             <requirement type="package" version="@VERSION@">bioconductor-minfi</requirement>
             <requirement type="package" version="0.4.0">bioconductor-illuminahumanmethylation450kmanifest</requirement>
-            <requirement type="package" version="1.40.6">bioconductor-rtracklayer</requirement>
+            <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>
             <yield />
         </requirements>
     </xml>
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_dmr.xml
--- a/minfi_dmr.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_dmr.xml	Mon May 20 07:14:26 2019 -0400
@@ -56,8 +56,8 @@
     </configfile>
     </configfiles>
     <inputs>
-        <param type="data" name="grset" format="rdata" label="Data Mapped To The Genome" help="This class (GenomicRatioSet) holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
-location." />
+        <param type="data" name="grset" format="rdata" label="Data Mapped To The Genome"
+            help="This class (GenomicRatioSet) holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location." />
         <param type="data" name="phenotype_table" format="tabular" label="Phenotype Table"
             help="Phenotype Table must include the following information: sampleID, phenotype and paird or unpaired samples column"/>
         <param name="maxgap_size" type="integer" value="250" label="maxGap Size"
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_dropsnp.xml
--- a/minfi_dropsnp.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_dropsnp.xml	Mon May 20 07:14:26 2019 -0400
@@ -24,8 +24,8 @@
     </configfile>
     </configfiles>
     <inputs>
-        <param type="data" name="grset" format="rdata" label="Genomic Ratio Set" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
-location."/>
+        <param type="data" name="grset" format="rdata" label="Genomic Ratio Set"
+            help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/>
     </inputs>
     <outputs>
         <data name="grsetwithoutsnp" format="rdata" from_work_dir="dropsnpGRSet.rdata" label="Data Mapped To The Genome without SNPs"/>
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_getbeta.xml
--- a/minfi_getbeta.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_getbeta.xml	Mon May 20 07:14:26 2019 -0400
@@ -22,8 +22,8 @@
     </configfile>
     </configfiles>
     <inputs>
-        <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
-location."/>
+        <param type="data" name="mset" format="rdata" label="MethylSet"
+            help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/>
     </inputs>
     <outputs>
         <data name="matrix" format="bedgraph" label="Beta Values Matrix"/>
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_getcn.xml
--- a/minfi_getcn.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_getcn.xml	Mon May 20 07:14:26 2019 -0400
@@ -21,8 +21,8 @@
     </configfile>
     </configfiles> 
     <inputs>
-        <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
-location."/>
+        <param type="data" name="mset" format="rdata" label="MethylSet"
+            help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/>
     </inputs>
     <outputs>
         <data name="matrix" format="txt" label="CN Value Matrix" />
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_getm.xml
--- a/minfi_getm.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_getm.xml	Mon May 20 07:14:26 2019 -0400
@@ -21,8 +21,8 @@
     </configfile>
     </configfiles>  
     <inputs>
-        <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
-location."/>
+        <param type="data" name="mset" format="rdata" label="MethylSet"
+            help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/>
     </inputs>
     <outputs>
         <data name="matrix" format="txt" label="M Value Matrix"/>
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_getsnp.xml
--- a/minfi_getsnp.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_getsnp.xml	Mon May 20 07:14:26 2019 -0400
@@ -12,7 +12,7 @@
     ]]>
     </command>
     <configfiles>
-    <configfile name="minfi_snp_script"><![CDATA[
+        <configfile name="minfi_snp_script"><![CDATA[
 require("minfi", quietly = TRUE)
 
 GRSet <- get(load('$grset'))
@@ -21,11 +21,11 @@
 
 write.table(snps, '$table')
   ]]> 
-    </configfile>
+        </configfile>
     </configfiles> 
-<inputs>
-        <param type="data" name="grset" format="rdata" label="Data Mapped To The Genome" help="This class (GenomicRatioSet) holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
-location."/>
+    <inputs>
+        <param type="data" name="grset" format="rdata" label="Data Mapped To The Genome"
+            help="This class (GenomicRatioSet) holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/>
     </inputs>
     <outputs>
         <data name="table" format="txt" label="SNPInfo Table"/>
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_maptogenome.xml
--- a/minfi_maptogenome.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_maptogenome.xml	Mon May 20 07:14:26 2019 -0400
@@ -12,7 +12,7 @@
     ]]>
     </command>
     <configfiles>
-    <configfile name="minfi_mtg_script"><![CDATA[ 
+        <configfile name="minfi_mtg_script"><![CDATA[ 
 require("minfi", quietly = TRUE)
 require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)
 
@@ -22,7 +22,7 @@
 
 save(GRSet,file = '$grset')
     ]]>
-    </configfile>
+        </configfile>
     </configfiles>
     <inputs>
         <param type="data" name="rset" format="rdata" label="Methylation Data to Map" help="This class holds preprocessed data for Illumina methylation microarrays." />
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_mset.xml
--- a/minfi_mset.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_mset.xml	Mon May 20 07:14:26 2019 -0400
@@ -21,13 +21,14 @@
 
      ]]> 
     </configfile>
-    </configfiles>  
- <inputs>
-        <param type="data" name="RGChannelSet" format="rdata" label="RGChannelSet" help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array."/>
- </inputs>
- <outputs>
+    </configfiles>
+    <inputs>
+        <param type="data" name="RGChannelSet" format="rdata" label="RGChannelSet"
+            help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array."/>
+    </inputs>
+    <outputs>
         <data name="MethylSet" format="rdata" label="MethylSet" />
- </outputs>
+    </outputs>
     <tests>
         <test>
             <param name="RGChannelSet" value="RGChannelSet.rdata"/>
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_ppfun.xml
--- a/minfi_ppfun.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_ppfun.xml	Mon May 20 07:14:26 2019 -0400
@@ -11,7 +11,7 @@
     ]]>
     </command>
     <configfiles>
-    <configfile name="minfi_pp_script"><![CDATA[
+        <configfile name="minfi_pp_script"><![CDATA[
 require("minfi", quietly = TRUE)
 RGSet <- get(load('$rgset'))
 
@@ -19,11 +19,11 @@
 
 save(GRSet,file = '$grset')
  ]]> 
-    </configfile>
-    </configfiles> 
-
-<inputs>
-        <param type="data" name="rgset" format="rdata" label="RGChannelSet" help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." />
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param type="data" name="rgset" format="rdata" label="RGChannelSet"
+            help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." />
     </inputs>
     <outputs>
         <data name="grset" format="rdata" label="GenomicRatioSet"/>
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_ppquantile.xml
--- a/minfi_ppquantile.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_ppquantile.xml	Mon May 20 07:14:26 2019 -0400
@@ -12,7 +12,7 @@
     ]]>
     </command>
     <configfiles>
-    <configfile name="minfi_pp_script"><![CDATA[
+        <configfile name="minfi_pp_script"><![CDATA[
 require("minfi", quietly = TRUE)
 RGSet <- get(load('$rgset'))
 
@@ -24,10 +24,11 @@
 save(GRSet,file = '$grset')
 
 ]]> 
-    </configfile>
-    </configfiles> 
- <inputs>
-        <param type="data" name="rgset" format="rdata" label="RGChannelSet" help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." />
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param type="data" name="rgset" format="rdata" label="RGChannelSet"
+            help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." />
     </inputs>
     <outputs>
         <data name="grset" format="rdata" label="GenomicRatioSet"/>
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_qc.xml
--- a/minfi_qc.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_qc.xml	Mon May 20 07:14:26 2019 -0400
@@ -10,7 +10,7 @@
      ]]>
     </command>
     <configfiles>
-      <configfile name="read_qc_script">
+        <configfile name="read_qc_script">
     <![CDATA[
 require("minfi", quietly = TRUE)
 
@@ -24,11 +24,11 @@
 plotQC(qc)
 dev.off()
     ]]>
-     </configfile>
-        </configfiles>
+        </configfile>
+    </configfiles>
     <inputs>
-        <param type="data" name="MethylSet" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
-location."/>
+        <param type="data" name="MethylSet" format="rdata" label="MethylSet"
+            help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/>
     </inputs>
     <outputs>
         <data name="qctab" format="txt" label="Quality Control Report"/>
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_read450k.xml
--- a/minfi_read450k.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_read450k.xml	Mon May 20 07:14:26 2019 -0400
@@ -1,16 +1,16 @@
 <tool id="minfi_read450k" name="Minfi Read 450k" version="2.1.0">
-  <description>load .IDAT files</description>
-  <requirements>
-  <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
+    <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'
+        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 '$read_idat_script'
       ]]></command>
       <configfiles>
       <configfile name="read_idat_script"><![CDATA[
@@ -37,10 +37,12 @@
             <output name="RGChannelSet" file="RGChannelSet.rdata"/>
         </test>
     </tests>
-                    <help><![CDATA[
-                      The tool load the binary 450K array “IDAT” raw files generated by the Illumina Scanner. In addition to the methylated and an unmethylated intensity values for each 450,000 CpG positions, IDAT file contains some extra info such as control probes.]]></help>
-                    <citations>
-                    <citation type="doi">10.18129/B9.bioc.illuminaio</citation>
-                      </citations>
-                      </tool>
-                      
+    <help><![CDATA[
+The tool load the binary 450K array “IDAT” raw files generated by the Illumina Scanner. In addition to the methylated and an unmethylated intensity values for each 450,000 CpG positions, IDAT file contains some extra info such as control probes.
+
+]]></help>
+    <citations>
+        <citation type="doi">10.18129/B9.bioc.illuminaio</citation>
+</citations>
+</tool>
+
diff -r 53aaf097238c -r 9c6fbb7d5a2a minfi_rset.xml
--- a/minfi_rset.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_rset.xml	Mon May 20 07:14:26 2019 -0400
@@ -9,9 +9,9 @@
         Rscript '$read_rset_script'
      ]]>
    </command>
- <configfiles>
-      <configfile name="read_rset_script">
-   <![CDATA[
+    <configfiles>
+        <configfile name="read_rset_script">
+<![CDATA[
 require("minfi", quietly = TRUE)
 MSet <- get(load('$mset'))
 
@@ -19,10 +19,10 @@
 
 save(RSet,file = '$rset')  
     ]]> </configfile>
-        </configfiles>
-  <inputs>
-        <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
-location."/>
+    </configfiles>
+    <inputs>
+        <param type="data" name="mset" format="rdata" label="MethylSet"
+            help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/>
     </inputs>
     <outputs>
         <data name="rset" format="rdata" label="RatioSet"/>