--- a/crossmap_bigwig.xml	Tue Sep 26 05:45:25 2017 -0400
+++ b/crossmap_bigwig.xml	Fri Oct 20 02:50:41 2017 -0400
@@ -8,47 +8,35 @@
     <expand macro="version_command"/>
 
     <command><![CDATA[
-        #set $input_file = str($seq_source.input)
+CrossMap.py bigwig
+'${chain_source.input_chain}'
+'${input}'
+'${output}'
 
-        CrossMap.py bigwig
-            '${chain_source.input_chain}'
-            '${input_file}'
-            '${output}'
-
-            && mv '${output}.bw' '${output}'
-
+&& mv '${output}.bw' '${output}'
     ]]></command>
 
     <inputs>
-        <conditional name="seq_source">
-            <expand macro="source" />
-            <when value="cached">
-                <param format="bigwig" name="input" type="data" label="BigWig file">
-                    <validator type="unspecified_build"/>
-                    <!-- Gives error in tests
-                    <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
-                    -->
-                </param>
-            </when>
-            <when value="history">
-                <param type="data" format="bigwig" name="input"       label="BigWig file"/>
-            </when>
-        </conditional>
+        <param name="input" type="data" format="bigwig" label="BigWig file"/>
+
         <expand macro="chain" />
     </inputs>
 
     <outputs>
-        <data format="bigwig" name="output" label="${tool.name} on ${on_string}" />
+        <data name="output" format="bigwig" label="${tool.name} on ${on_string}" />
     </outputs>
 
     <tests>
-    <!-- BigWig --><!-- Malfuncioning in CrossMap 0.2, but patched via galaxy toolshed installer -->
         <test>
-            <param name="input_format" value="bigwig"/>
+            <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
             <param name="index_source" value="history"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+
+            <output name="output" file="test_bigwig_01_output_a.bw"/>
+        </test>
+        <test><!-- cached chain file -->
             <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
-            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
-            <param name="include_fails" value="False"/>
+            <param name="index_source" value="cached"/>
 
             <output name="output" file="test_bigwig_01_output_a.bw"/>
         </test>
@@ -59,16 +47,15 @@
 BigWig
 ------
 
-    Input wiggle data can be in variableStep (for data with irregular
-    intervals) or fixedStep (for data with regular intervals). Regardless of
-    the input, the output will always in bedGraph format. bedGraph format is
-    similar to wiggle format and can be converted into BigWig format using UCSC
-    wigToBigWig tool. We export files in bedGraph because it is usually much
-    smaller than file in wiggle format, and more importantly, CrossMap
-    internally transforms wiggle into bedGraph to increase running speed.
+Input wiggle data can be in variableStep (for data with irregular
+intervals) or fixedStep (for data with regular intervals). Regardless of
+the input, the output will always in bedGraph format. bedGraph format is
+similar to wiggle format and can be converted into BigWig format using UCSC
+wigToBigWig tool. We export files in bedGraph because it is usually much
+smaller than file in wiggle format, and more importantly, CrossMap
+internally transforms wiggle into bedGraph to increase running speed.
 
-Please see `the manual <http://crossmap.sourceforge.net/#convert-wiggle-bigwig-format-files>`__ for more details
-]]></help>
+    ]]></help>
 
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt730</citation>