--- a/multigps.xml	Thu Apr 06 11:26:41 2017 -0400
+++ b/multigps.xml	Sun Dec 22 17:11:12 2019 +0000
@@ -3,9 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="0.74">multigps</requirement>
-    </requirements>
+    <expand macro="requirements" />
     <command detect_errors="aggressive">
         <![CDATA[
             #set output_dir = $output_html.files_path
@@ -20,7 +18,11 @@
             ## Do not run the parallel version of meme.
             --meme1proc
             --threads \${GALAXY_SLOTS:-4}
-            --geninfo '$chromInfo'
+            #if str($in_test_mode) == "no":
+                --geninfo '$chromInfo'
+            #else:
+                --geninfo '$__tool_directory__/tool-data/hg19.len'
+            #end if
             ## Advanced options
             #set aoc = $advanced_options_cond
             #if str($aoc.advanced_options) == 'display':
@@ -410,6 +412,8 @@
             </when>
             <when value="hide" />
         </conditional>
+        <!-- Functional testing -->
+        <param name="in_test_mode" type="hidden" value="no" />
     </inputs>
     <outputs>
         <data name="output_design_file" format="tabular" label="${tool.name} (design file) on ${on_string}">
@@ -428,6 +432,7 @@
                 </repeat>
             </repeat>
             <param name="advanced_options" value="hide" />
+            <param name="in_test_mode" value="yes" />
             <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/>
             <output name="output_bed" file="hg19_output_bed1.bed" ftype="bed"/>
             <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
@@ -443,6 +448,7 @@
                 </repeat>
             </repeat>
             <param name="advanced_options" value="display" />
+            <param name="in_test_mode" value="yes" />
             <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/>
             <output name="output_bed" file="hg19_output_bed2.bed" ftype="bed"/>
             <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
@@ -466,7 +472,7 @@
 
 * **Loading data:**
 
- - **Optional file containing reads from a control experiment** - must be same format as input experiment
+ - **Optional file containing reads from a control experiment** - file containing reads from a control experiment
  - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model).
  - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be.
  - **Use non-unique reads** - Use non-unique reads.
@@ -520,23 +526,7 @@
 
     </help>
     <citations>
-        <citation type="bibtex">
-            @article{Mahony2014,
-            journal = {PLOS Computational Biology},
-            author = {1. Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H, Gifford DK},
-            title = {An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding},
-            year = {2014},}
-            volume = {10},
-            number = {3},
-            pages = {e1003501},}
-        </citation>
-        <citation type="bibtex">
-            @article{Liang2012,
-            journal = {BMC Bioinformatics},
-            author = {2. Liang, Ketes},
-            title = {Normalization of ChIP-seq data with control},
-            year = {2012},}
-        </citation>
+        <citation type="doi">10.1371/journal.pcbi.1003501</citation>
     </citations>
 </tool>