changeset 64:3d083550977f draft

Uploaded

--- a/minfi_dmp.xml	Thu Apr 04 11:20:23 2019 -0400
+++ b/minfi_dmp.xml	Thu Apr 04 11:21:19 2019 -0400
@@ -29,13 +29,9 @@
 
 tab <- tab[,-(11:14),drop=FALSE] 
 
-colnames(tab) <- c("seqname","source","feature","start","end","score","strand", "frame","attributes", "names")
-
-tab[,"source"] <- NULL
+tab <- tab[,c(1,4,5,10)]
 
-tab[,"frame"] <- NULL
-
-tab[,"attributes"] <- NULL
+colnames(tab) <- c('chr','start','end','names')
 
 dmp <- dmpFinder(beta, pheno[,"V2"], type = type, qCutoff = qCutoff, shrinkVar = shrinkVar)
 
@@ -43,10 +39,10 @@
 
 data <- merge(dmp, tab, by="names",sort = TRUE)
 
-data <- data[c("seqname","start","end","names","score","strand", "feature","intercept", "f", "pval","qval")]
+data <- data[,c(6,7,8,1,4,5)]  
 
-write.table(data, file= '$dmp', quote = FALSE,col.names = FALSE, row.names = FALSE, sep = "\t")
-    ]]>
+write.table(data, file= '$dmp', quote = FALSE,col.names = TRUE, row.names = FALSE, sep = "\t")
+]]>
         </configfile>
     </configfiles> 
     <inputs>
@@ -56,13 +52,13 @@
             <option value="categorical">categorical</option>
             <option value="continuous">continuous</option>
         </param> 
-        <param name="q_cutoff" type="integer" value="1" label="qCutoff Size" help="DMPs with an FDR q-value greater than this will not be returned."/>
+        <param name="q_cutoff" type="float" value="1" label="qCutoff Size" help="DMPs with an FDR q-value greater than this will not be returned."/>
         <param name="variance_shrinkage" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Variance Shrinkage"
             help="Enable variance shrinkage is recommended when sample sizes are small"/>
         <param type="data" name="ucsc_genome" format="gtf" label="Genome Table" help="UCSC genome data Methyl450"/>
     </inputs>
     <outputs>
-        <data name="dmp" format="interval" label="Differentially Methylated Positions"/>
+       <data name="dmp" format="interval" label="Differentially Methylated Positions"/>
     </outputs>
     <tests>
         <test>
@@ -80,17 +76,12 @@
 
 The output is an interval file with the following columns:
 
-    - seqnames
+    - chr
     - start
     - end
-    - cpg
     - names
-    - score
-    - strand
-    - feature
-    - intercept
-    - f pval
-    - qval
+    - pvalue
+    - qval 
 
  ]]></help>
     <expand macro="citations" />