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changeset 75:9c6fbb7d5a2a draft

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planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
author kpbioteam
date Mon, 20 May 2019 07:14:26 -0400
parents 53aaf097238c
children fef50103f6b3
files macros.xml minfi_dmr.xml minfi_dropsnp.xml minfi_getbeta.xml minfi_getcn.xml minfi_getm.xml minfi_getsnp.xml minfi_maptogenome.xml minfi_mset.xml minfi_ppfun.xml minfi_ppquantile.xml minfi_qc.xml minfi_read450k.xml minfi_rset.xml
diffstat 14 files changed, 68 insertions(+), 64 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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"
--- 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"/>
--- 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"/>
--- 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" />
--- 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"/>
--- 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"/>
--- 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." />
--- 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"/>
--- 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 = '$grset')
  ]]> 
-    </configfile>
-    </configfiles> 
-
-<inputs>
-        <param type="data" name="rgset" format="rdata" label="RGChannelSet" help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." />
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param type="data" name="rgset" format="rdata" label="RGChannelSet"
+            help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array." />
     </inputs>
     <outputs>
         <data name="grset" format="rdata" label="GenomicRatioSet"/>
--- a/minfi_ppquantile.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_ppquantile.xml	Mon May 20 07:14:26 2019 -0400
@@ -12,7 +12,7 @@
     ]]>
     </command>
     <configfiles>
-    <configfile name="minfi_pp_script"><![CDATA[
+        <configfile name="minfi_pp_script"><![CDATA[
 require("minfi", quietly = TRUE)
 RGSet <- get(load('$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"/>
--- 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"/>
--- 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 '$read_idat_script'
       ]]></command>
       <configfiles>
       <configfile name="read_idat_script"><![CDATA[
@@ -37,10 +37,12 @@
             <output name="RGChannelSet" file="RGChannelSet.rdata"/>
         </test>
     </tests>
-                    <help><![CDATA[
-                      The tool load the binary 450K array “IDAT” raw files generated by the Illumina Scanner. In addition to the methylated and an unmethylated intensity values for each 450,000 CpG positions, IDAT file contains some extra info such as control probes.]]></help>
-                    <citations>
-                    <citation type="doi">10.18129/B9.bioc.illuminaio</citation>
-                      </citations>
-                      </tool>
-                      
+    <help><![CDATA[
+The tool load the binary 450K array “IDAT” raw files generated by the Illumina Scanner. In addition to the methylated and an unmethylated intensity values for each 450,000 CpG positions, IDAT file contains some extra info such as control probes.
+
+]]></help>
+    <citations>
+        <citation type="doi">10.18129/B9.bioc.illuminaio</citation>
+</citations>
+</tool>
+
--- a/minfi_rset.xml	Thu May 16 08:56:35 2019 -0400
+++ b/minfi_rset.xml	Mon May 20 07:14:26 2019 -0400
@@ -9,9 +9,9 @@
         Rscript '$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"/>