changeset 4:0d1957068766 draft

Uploaded

--- a/findDMR/findDMR.R	Mon Feb 06 10:44:03 2017 -0500
+++ b/findDMR/findDMR.R	Mon Feb 20 08:32:26 2017 -0500
@@ -6,8 +6,8 @@
 
 args <- commandArgs(trailingOnly = TRUE)
 GSMTable = args[1]
-IlmnTable = args[2]
-gmTable = args[3]
+platform = args[2]
+Data_Table = args[3]
 cutoff = as.numeric(args[4])
 clusterSize = as.numeric(args[5])
 DMR = args[6]
@@ -15,9 +15,9 @@
 #GSMTable<-("test-data/input.csv")
 TAB = fread(GSMTable)
 #IlmnTable <- ("test-data/IlmnTable.csv")
-IlmnInfo = fread(IlmnTable)
+IlmnInfo = fread(platform)
 #gmTable<-("test-data/gmTable.csv")
-gmSet = fread(gmTable)
+gmSet = fread(Data_Table)
 
 # bumphunter Run with processed data
 designMatrix <- model.matrix( ~ TAB$Phenotype)

--- a/findDMR/findDMR.xml	Mon Feb 06 10:44:03 2017 -0500
+++ b/findDMR/findDMR.xml	Mon Feb 20 08:32:26 2017 -0500
@@ -1,6 +1,6 @@
 <tool id="DMR" name="findDMR" version="1.16.2">
   <description>
-from series of samples 
+from series of samples
   </description>
   <requirements>
          <requirement type="package" version="3.2.1">R</requirement>
@@ -8,15 +8,15 @@
 <stdio>
    <exit_code range="1:" />
 </stdio>
-  <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$IlmnTable" "$gmTable" "$cutoff" "$clusterSize" "$DMR"</command>
+  <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</command>
   <inputs>
     <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable">
       <validator type="empty_field" message="This field is required."/>
     </param>
-     <param optional="false" format="csv" name="IlmnTable" type="data" value="" help="CG, CHR, BP table." label="[required] IlmnTable">
+     <param optional="false" format="csv" name="platform" type="data" value="" help="CG, CHR, BP table." label="[required] platform">
       <validator type="empty_field" message="This field is required."/>
     </param>
-     <param optional="false" format="csv" name="gmTable" type="data" value="" help="gmSet of data." label="[required] gmTable">
+     <param optional="false" format="csv" name="Data_Table" type="data" value="" help="Matrix of data." label="[required] Data_Table">
       <validator type="empty_field" message="This field is required."/>
     </param>
     <param name="cutoff" type="float" value=""
@@ -37,8 +37,8 @@
       <element name="test-data">
           <collection type="data">
               <element name="GSMTable" value="test-data/input.csv"/>
-              <element name="IlmnTable" value="test-data/IlmnTable.csv"/>
-              <element name="gmTable" value="test-data/gmTable.csv"/>
+              <element name="platform" value="test-data/platform.csv"/>
+              <element name="Data_Table" value="test-data/Data_Table.csv"/>
               <element name="cutoff" value="0.2"/>
               <element name="clusterSize" value="2"/>
           </collection>