# HG changeset patch
# User ning
# Date 1363386107 14400
# Node ID 03aa1c6fe091805635e14b28e6a60724a8325e89
# Parent  c85f281dc05977a188c6ab18378b83d140819b35
Uploaded

diff -r c85f281dc059 -r 03aa1c6fe091 EBIsoformMultiCondTest.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/EBIsoformMultiCondTest.xml	Fri Mar 15 18:21:47 2013 -0400
@@ -0,0 +1,37 @@
+<tool id="EBIsoformMultiCondTest" name="Isoform level DE test across multiple conditions">
+  <description>Runs EBSeq to find DE isoforms across multiple (more than two) conditions</description>
+  <command>R --quiet --slave --file=$GALAXY_ROOT_DIR/tools/EBSeq/EBIsoformMultiCondTest.R --args $Isoform_Expression $First_Row_Sample_Names $Conditions $Ig_Vector $Patterns_of_Interests $PP_of_each_pattern $Pattern_with_highest_PP $Sizes</command>
+  <inputs>
+		<param name="Isoform_Expression" type="data" format="tabular" label="Isoform Expression (tab eliminated)"/>
+		<param name="First_Row_Sample_Names" type="select" format="text">
+			<label>The First Row is Sample Names?</label>
+			<option value="y">Yes</option>
+			<option value="n">No</option>
+			</param>
+		<param name="Conditions" type="text" size="60" value="C1,C2" label="Enter which condition each
+			sample belongs to (seperated by comma, no space please)." 
+			help=""/>
+		<param name="Ig_Vector" type="data" format="tabular" label="Ig Vector to define the uncertainty groups"/>
+		<param name="Patterns_of_Interests" type="data" format="tabular" label="Patterns of Interests"/>
+  </inputs>
+  <outputs>
+		<data format="tabular" name="PP_of_each_pattern" />
+		<data format="tabular" name="Pattern_with_highest_PP" />
+                <data format="tabular" name="Sizes" />
+  </outputs>
+
+  <help>
+The input Conditions should have exactly two levels. The length of the Condition vector should be exactly the same as the number of columns in the data file (except the isoform names column).
+
+The patterns of interests could be obtained by function Get All Possible Patterns (and optionally, if there are too many patterns generated, the function Choose Patterns could be used to choose only subset of the patterns.)
+
+The Ig Vector could be generated by the GetIg function or obtained from RSEM output.
+
+Three output files will be generated. The first file contains the Posterior probability of being each pattern.
+The second file contains the pattern with highest PP for each isoform and the normalized expressions.Isoforms are with the same order as in input file.
+The last file provides the library size factor for each sample.
+
+</help>
+
+
+</tool>