# HG changeset patch
# User saharlcc
# Date 1474336717 14400
# Node ID babf45f7c9a35427292f5f01ec24aa77468ddc91
# Parent  581e4c6b483f5c8431ec803c8a7b96f1dcedb38a
Uploaded

diff -r 581e4c6b483f -r babf45f7c9a3 isoDE.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/isoDE.xml	Mon Sep 19 21:58:37 2016 -0400
@@ -0,0 +1,79 @@
+<tool id="isoDE" name="IsoDE2">
+  <description>Compute gene Differential Expression based on IsoEM2 output </description>
+  <command interpreter="bash">isoDE2.sh
+      -c1
+      $condition1
+      #for $r in $condition1replicates
+        ${r.c1Rep}
+      #end for
+      -c2
+      $condition2
+      #for $r in $condition2replicates
+        ${r.c2Rep}
+      #end for
+      -pval $pval
+      -geneFPKMout $geneFPKM
+	-geneTPMout $geneTPM
+	-isoFPKMout $isoformFPKM  
+	-isoTPMout $isoformTPM
+ </command>
+
+  <inputs>
+  <param name="condition1" type="data" label="Select data for Condition 1" format="gz" help="Condition 1 isoEM2 compressed output file"/>
+<!--
+    <param format="toolshed.gz" name="condition1" type="data" label="Select data for Condition 1" help="Condition 1 isoEM2 compressed output file"/>
+-->
+    <repeat name="condition1replicates" title="Replicates for Condition 1">
+      <param name="c1Rep" label="Add replicate" type="data" format="gz" data_ref="condtion1" />
+    </repeat>
+
+    <param format="gz" name="condition2" type="data" label="Select data for Condition 2"  help="Condition 2 isoEM2 compressed output file"/>
+<!--
+    <param  format="toolshed.gz" name="condition2" type="data" label="Select data for Condition 2" help="Condition 2 IsoEM2 compressed output file"/>
+-->
+    <repeat name="condition2replicates" title="Replicates for Condition 2">
+      <param format="gz" name="c2Rep" label="Add replicate" type="data" data_ref="condtion2" />
+    </repeat>
+
+
+    <param name="pval" label="p-value" type="float" value="0.05" help="Desired p-value to for which a reliable fold change level will be reported" />
+
+  </inputs>
+  <outputs>
+    <data format="tabular" name="geneFPKM" label="isoDE gene fpkm"  />
+    <data format="tabular" name="isoformFPKM" label="isoDE isoform fpkm"  />
+    <data format="tabular" name="geneTPM" label="isoDE gene tpm"  />
+    <data format="tabular" name="isoformTPM" label="isoDE isoform tpm"  />
+  </outputs>
+
+<help>
+**What it does**
+
+Computes gene and isoform differential expression between two conditions (example tumor and normal) for both Fragment per Kilobase of transcript length per Million 
+bases (FPKM) and Transcripts per Million (TPM) values. The computation is based on the boostraping output generated by IsoEM2. The number of bootstrap iterations for 
+IsoEM2 should be >= 20 (suggested 200).
+
+**Input**
+
+* - One or more IsoEM output files (compressed tar files) for each of the two conditions. More than one file can be used if there are replicated for either condition
+* - Desired p-value to for which a reliable fold change level will be reported
+*
+
+
+
+
+**Output**
+
+* four output files containinag results for Gene FPKM DE, Gene TPM DE, Isoform FPKM DE, and Isoform TPM DE. The four files have identical format with the following fields
+* 1- Gene/isoform ID
+* 2- Reliable log_2(FC) : conservative estimate of fold change in log base 2. 
+*               For the confidence level specified by the input p-value, fold change of gene/isoform abundance (FPKM/TPM) in condition 2 compared condition 1 is 
+*               at least 2 ^ absoulte value of this field.The sign indicates the direction, +ve means over expressed in condition 2, -ve means underexpressed in
+*               condition 1. NDE indicates that no change was detected.
+* 3- log_2(condition 1 FPKM (or TPM)/condition 1 FPKM(or TPM)) based on IsoEM2 run without bootstrapping
+* 4- condition 1 FPKM (or TPM) based on IsoEM2 run without bootstrapping
+* 5- condition 2 FPKM (or TPM) based on IsoEM2 run without bootstrapping
+
+
+</help>
+</tool>