| Previous changeset 4:0d1957068766 (2017-02-20) Next changeset 6:a0e3f4efb03f (2017-04-25) |
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Commit message:
Uploaded |
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modified:
findDMR/findDMR.R findDMR/findDMR.xml |
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removed:
findDMR/test-data/._.DS_Store findDMR/test-data/IlmnTable.csv findDMR/test-data/gmTable.csv |
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| diff -r 0d1957068766 -r 715d03e1fd83 findDMR/findDMR.R --- a/findDMR/findDMR.R Mon Feb 20 08:32:26 2017 -0500 +++ b/findDMR/findDMR.R Mon Mar 20 06:51:59 2017 -0400 |
| [ |
| @@ -12,11 +12,10 @@ clusterSize = as.numeric(args[5]) DMR = args[6] -#GSMTable<-("test-data/input.csv") TAB = fread(GSMTable) -#IlmnTable <- ("test-data/IlmnTable.csv") + IlmnInfo = fread(platform) -#gmTable<-("test-data/gmTable.csv") + gmSet = fread(Data_Table) # bumphunter Run with processed data @@ -35,7 +34,7 @@ DMRInfo <- data.table(DMRTable$chr, DMRTable$start, DMRTable$end) -#DMR<-("test-data/DMR.bed") + write.table( DMRInfo, DMR, |
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| diff -r 0d1957068766 -r 715d03e1fd83 findDMR/findDMR.xml --- a/findDMR/findDMR.xml Mon Feb 20 08:32:26 2017 -0500 +++ b/findDMR/findDMR.xml Mon Mar 20 06:51:59 2017 -0400 |
| [ |
| @@ -10,13 +10,13 @@ </stdio> <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"> + <param optional="false" format="txt" 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="platform" type="data" value="" help="CG, CHR, BP table." label="[required] platform"> + <param optional="false" format="txt" 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="Data_Table" type="data" value="" help="Matrix of data." label="[required] Data_Table"> + <param optional="false" format="txt" 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="" @@ -36,9 +36,9 @@ <param name="test"> <element name="test-data"> <collection type="data"> - <element name="GSMTable" value="test-data/input.csv"/> - <element name="platform" value="test-data/platform.csv"/> - <element name="Data_Table" value="test-data/Data_Table.csv"/> + <element name="GSMTable" value="test-data/input.txt"/> + <element name="platform" value="test-data/platform.txt"/> + <element name="Data_Table" value="test-data/Data_Table.txt"/> <element name="cutoff" value="0.2"/> <element name="clusterSize" value="2"/> </collection> |
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| diff -r 0d1957068766 -r 715d03e1fd83 findDMR/test-data/._.DS_Store |
| b |
| Binary file findDMR/test-data/._.DS_Store has changed |
| b |
| diff -r 0d1957068766 -r 715d03e1fd83 findDMR/test-data/IlmnTable.csv --- a/findDMR/test-data/IlmnTable.csv Mon Feb 20 08:32:26 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,485578 +0,0 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|
| b |
| diff -r 0d1957068766 -r 715d03e1fd83 findDMR/test-data/gmTable.csv --- a/findDMR/test-data/gmTable.csv Mon Feb 20 08:32:26 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,485578 +0,0 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