--- a/hicCorrectMatrix.xml	Mon Apr 03 07:06:43 2017 -0400
+++ b/hicCorrectMatrix.xml	Thu Nov 02 11:10:27 2017 -0400
@@ -5,8 +5,8 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command>
-<![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
+
         ln -s '$matrix' temp_matrix.npz.h5 &&
 
         hicCorrectMatrix
@@ -50,7 +50,7 @@
                     --xMax $mode.xMax
                 #end if
                 #if $mode.filterThreshold_low and $mode.filterThreshold_large:
-                    --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large
+                    --filterThreshold '$mode.filterThreshold_low' '$mode.filterThreshold_large'
                 #end if
             #else:
                 --plotName diagnostic_plot.png
@@ -101,10 +101,12 @@
             </when>
         </conditional>
 
-        <repeat name="chromosomes" min="1"
+        <repeat name="chromosomes" min="0"
             title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
                     The order of the given chromosomes will be kept for the resulting corrected matrix">
-            <param name="chromosome" type="text" value="" />
+            <param name="chromosome" type="text" value="" >
+                <validator type="empty_field" />
+            </param>
         </repeat>
 
     </inputs>
@@ -118,7 +120,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="matrix" value="hicBuildMatrix_result1.h5" ftype="h5"/>
+            <param name="matrix" value="small_test_matrix.h5" ftype="h5"/>
             <param name="mode_selector" value="correct"/>
             <repeat name="chromosomes">
                 <param name="chromosome" value="chrUextra"/>
@@ -129,7 +131,7 @@
             <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>
         </test>
         <test>
-            <param name="matrix" ftype="h5" value="hicBuildMatrix_result1.h5"/>
+            <param name="matrix" ftype="h5" value="small_test_matrix.h5"/>
             <param name="mode_selector" value="diagnostic_plot"/>
             <repeat name="chromosomes">
                 <param name="chromosome" value="chrUextra"/>
@@ -144,18 +146,16 @@
 
 **What it does**
 
-Runs Dekker's iterative correction over a hic matrix.
+Runs Dekker's iterative correction over a Hi-C matrix.
 
+correct:         Run the iterative correction.
 
-    correct        Run the iterative correction.
-    diagnostic_plot
-                   Plots a histogram of the coverage per bin together with the
-                   modified z-score based on the median absolute deviation
-                   method (see Boris Iglewicz and David Hoaglin 1993, Volume
-                   16: How to Detect and Handle Outliers The ASQC Basic
-                   References in Quality Control: Statistical Techniques,
-                   Edward F. Mykytka, Ph.D., Editor.
-
+diagnostic_plot:  Plots a histogram of the coverage per bin together with the
+modified z-score based on the median absolute deviation
+method (see Boris Iglewicz and David Hoaglin 1993, Volume
+16: How to Detect and Handle Outliers The ASQC Basic
+References in Quality Control: Statistical Techniques,
+Edward F. Mykytka, Ph.D., Editor.
 
 ]]></help>
     <expand macro="citations" />