# HG changeset patch
# User fubar
# Date 1371282586 14400
# Node ID 697272b8ef420260065ab9862231067a9f28e5ec
# Parent  4afd763390e6982a16961831405937d776c355a4
Uploaded

diff -r 4afd763390e6 -r 697272b8ef42 rgedgeR/rgedgeRpaired.xml
--- a/rgedgeR/rgedgeRpaired.xml	Thu Jun 13 01:51:54 2013 -0400
+++ b/rgedgeR/rgedgeRpaired.xml	Sat Jun 15 03:49:46 2013 -0400
@@ -26,7 +26,7 @@
     <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True" 
          multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true">
     </param>
-    <param name="subjectids" type="text" optional="true" size="120"
+    <param name="subjectids" type="text" optional="true" size="120" value = ""
        label="IF SUBJECTS NOT ALL INDEPENDENT! Enter integers to indicate sample pairing for every column in input"
        help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter '1,2,1,2'">
       <sanitizer>
@@ -65,14 +65,16 @@
 <param name='input1' value='test_bams2mx.xls' ftype='tabular' />
  <param name='treatment_name' value='case' />
  <param name='title' value='edgeRtest' />
+ <param name='useNDF' value='' />
  <param name='fdrtype' value='fdr' />
  <param name='priordf' value="0" />
  <param name='fdrthresh' value="0.05" />
  <param name='control_name' value='control' />
- <param name='Treat_cols' value='3,4,5,9' />
+ <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' ftype='tabular' compare='diff' />
- <output name='html_file' file='edgeRtest1out.html' ftype='html' compare='diff' lines_diff='20' />
+ <output name='outtab' file='edgeRtest1out.xls' compare='diff' />
+ <output name='html_file' file='edgeRtest1out.html'  compare='diff' lines_diff='20' />
 </test>
 </tests>