--- a/footprint.xml	Tue May 02 15:05:59 2017 -0400
+++ b/footprint.xml	Mon Nov 20 05:04:27 2017 -0500
@@ -3,49 +3,31 @@
     <requirements>
         <requirement type="package" version="1.0.0">footprint</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command><![CDATA[
-            ln -s '$bam_file' ./bam_file.bam
-
-            &&
-
-            find_footprints.sh
-
-            ./bam_file.bam
-
-            '$chrom_sizes'
-
-            '$motif_coords'
+    <command detect_errors="aggressive"><![CDATA[
+ln -s '$bam_file' ./bam_file.bam
+&&
+find_footprints.sh
+    ./bam_file.bam
+    '$chrom_sizes'
+    '$motif_coords'
+    ## genome source
+    #if $refGenomeSource.genomeSource == "history":
+        '$refGenomeSource.ownFile'
+    #else
+        '$refGenomeSource.builtin.fields.path'
+    #end if
+    '$factor_name'
+    '$bias_file'
+    '$peak_file'
+    $no_of_components
+    $background
+    $fixed_bg
+    &&
+mv *.PARAM PARAM &&
+mv *.RESULTS RESULTS &&
+mv *.plot2.png plot2.png &&
+mv *.plot1.png plot1.png
 
-            ## genome source
-            #if $refGenomeSource.genomeSource == "history":
-                '$refGenomeSource.ownFile'
-            #else
-                '$refGenomeSource.builtin.fields.path'
-            #end if
-
-            $factor_name
-
-            '$bias_file'
-
-            '$peak_file'
-
-            $no_of_components
-
-            $background
-
-            $fixed_bg
-
-            &&
-            mv *.PARAM PARAM
-            &&
-            mv *.RESULTS RESULTS
-            &&
-            mv *.plot2.png plot2.png
-            &&
-            mv *.plot1.png plot1.png
 ]]>
     </command>
     <inputs>
@@ -125,7 +107,6 @@
 
 This is a pipeline to find transcription factor footprints in ATAC-seq or DNase-seq data.
 
-
 -----
 
 .. class:: infomark
@@ -144,6 +125,7 @@
  * A 6-column bed file with the coordinates of motif matches (eg resulting from scanning the genome with a PWM) for the transcription factor of interest.
  * The 6 columns should contain chromosome, start coordinate, end coordinate, name, score and strand information in this order. The coordinates should be closed (1-based).
  * Example: chr1    24782   24800   .       11.60   -
+ * There should not be any additional columns.
 
 transcription factor
  * The name of the transcription factor of interest supplied by the user, e.g. CTCF.
@@ -172,6 +154,7 @@
  * Whether the background component should be kept fixed.
  * Options are TRUE or FALSE.
  * Setting "TRUE" keeps this component fixed, whereas setting "FALSE" lets it be reestimated during training.
+ * In general, if the background is estimated from bias (option "Seq"), it is recommended to keep it fixed.
 
 -----
 
@@ -201,7 +184,7 @@
 ]]></help>
     <citations>
         <citation type="bibtex">@ARTICLE{footprint,
-        author = {Aslihan Karabacak and Uwe Ohler},
+        author = {Aslihan Karabacak, Galip Gurkan Yardimci, Ricardo Wurmus, Dilmurat Yusuf, Uwe Ohler},
         title = {To submit},
         journal = {},
         year = {},