# HG changeset patch
# User fubar
# Date 1374902883 14400
# Node ID a4edc1360ea9725394bf4b014846710fb97ecb7f
# Parent  8c0405de0695da0cc1b058db442319e33dfe3e01
Uploaded

diff -r 8c0405de0695 -r a4edc1360ea9 rgedgeR/rgedgeRpaired.xml
--- a/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 01:25:20 2013 -0400
+++ b/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 01:28:03 2013 -0400
@@ -9,7 +9,7 @@
   
   <command interpreter="python">
      rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts" 
-    --output_dir "$html_file.files_path" --output_html "$html_file" --output_tab "$outtab" --make_HTML "yes"
+    --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
   </command>
   <inputs>
     <param name="input1"  type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
@@ -94,10 +94,10 @@
   </inputs>
   <outputs>
     <data format="tabular" name="out_edgeR" label="${title}_topTable_edgeR.xls">
-         <filter>edgeR.doedgeR == "T"</filter>
+         <filter>doedgeR == "T"</filter>
     </data>
     <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls">
-         <filter>DESeq2.doDESeq2 == "T"</filter>
+         <filter>doDESeq2 == "T"</filter>
     </data>
     <data format="tabular" name="out_VOOM" label="${title}_topTable_VOOM.xls">
          <filter>doVoom == "T"</filter>
@@ -123,7 +123,7 @@
  <param name='subjectids' value='' />
   <param name='Treat_cols' value='3,4,5,9' />
  <param name='Control_cols' value='2,6,7,8' />
- <output name='outtab' file='edgeRtest1out.xls' compare='diff' />
+ <output name='out_edgeR' file='edgeRtest1out.xls' compare='diff' />
  <output name='html_file' file='edgeRtest1out.html'  compare='diff' lines_diff='20' />
 </test>
 </tests>
@@ -686,7 +686,6 @@
 TreatmentCols = "$Treat_cols"
 ControlName = "$control_name"
 ControlCols= "$Control_cols"
-outputfilename = "$outtab"
 org = "$input1.dbkey"
 if (org == "") { org = "hg19"}
 fdrtype = "$fdrtype"