# HG changeset patch
# User saharlcc
# Date 1474337381 14400
# Node ID dc8efad9c31b3252ef969ee2cd0836a9168f899a
# Parent  aa9875d90894f0dc028968f06fa850a2e936feb1
Uploaded

diff -r aa9875d90894 -r dc8efad9c31b FC_Filter_IsoDE_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FC_Filter_IsoDE_wrapper.xml	Mon Sep 19 22:09:41 2016 -0400
@@ -0,0 +1,56 @@
+<tool id="FC_Filter_IsoDE2" name="Fold Change Filter">
+  <description>Filters IsoDE2 output based on fold change</description>
+  <command interpreter="bash">
+     FC_Filter_IsoDE_wrapper.sh $input1 $input2 $out_file $FC_min
+  </command>
+  <inputs>  
+
+    <param name="input1" type="data" label="Select data from IsoDE output files" />
+    <param name="input2" type="select" label="A list of genes/isoforms over expressed in:">
+      <option value="1">Condition 1</option>
+      <option value="2">Condition 2</option>
+      <option value="3">Condition 1 or Condition 2</option>
+    </param>
+    <param name="FC_min" type="integer" value="2" label="Minimum Fold change:" />
+  </inputs> 
+
+  <outputs>
+    <data format="tabular" name="out_file" metadata_source="input1" label="Filtered IsoDE"  />
+  </outputs>
+
+
+<help>  
+**What it does**
+
+This filter selects from the IsoDE2 output file, genes that genes that have fold change (ratio between the gene expression in the two conditions in comparison) greater 
+than or equal to the a certain threshold set by the user.
+
+
+**Input**
+
+* 1- IsoDE2 output file. It can be any of the output files generated by an IsoDE2 runs; for genes or isoforms/FPKM or TPM
+* 2- Direction of over expression of interest to the user (genes over expressed in condition1, over expressed in condition 2, or overexpressed in either condition)
+* 3- Minimim fold change of interest
+*
+*
+
+
+
+
+**Output**
+
+
+The output is a tabular file with the same fields as the input file, containing the subset of genes satisfying the conditions specified by the used.
+
+</help>
+</tool>
+
+
+
+
+
+
+
+
+
+