| Previous changeset 3:42cfcac7779d (2017-02-06) Next changeset 5:715d03e1fd83 (2017-03-20) |
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findDMR/findDMR.R findDMR/findDMR.xml |
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| diff -r 42cfcac7779d -r 0d1957068766 findDMR/findDMR.R --- a/findDMR/findDMR.R Mon Feb 06 10:44:03 2017 -0500 +++ b/findDMR/findDMR.R Mon Feb 20 08:32:26 2017 -0500 |
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| @@ -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) |
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| diff -r 42cfcac7779d -r 0d1957068766 findDMR/findDMR.xml --- a/findDMR/findDMR.xml Mon Feb 06 10:44:03 2017 -0500 +++ b/findDMR/findDMR.xml Mon Feb 20 08:32:26 2017 -0500 |
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| @@ -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> |