--- a/crossmap_bigwig.xml	Thu Jan 20 04:31:28 2022 +0000
+++ b/crossmap_bigwig.xml	Mon Sep 02 12:00:58 2024 +0000
@@ -6,36 +6,30 @@
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>
-
     <command><![CDATA[
-CrossMap.py bigwig
+CrossMap bigwig
 '${chain_source.input_chain}'
 '${input}'
 output
     ]]></command>
-
     <inputs>
         <param name="input" type="data" format="bigwig" label="BigWig file"/>
-
-        <expand macro="chain" />
+        <expand macro="chain"/>
     </inputs>
-
     <outputs>
-        <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" />
+        <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw"/>
     </outputs>
-
     <tests>
         <test>
             <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 -->
+        <test>
+            <!-- cached chain file -->
             <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig" dbkey="hg18"/>
             <param name="index_source" value="cached"/>
-
             <output name="output" file="test_bigwig_01_output_a.bw"/>
         </test>
     </tests>
@@ -53,7 +47,6 @@
 smaller than file in wiggle format, and more importantly, CrossMap
 internally transforms wiggle into bedGraph to increase running speed.
     ]]></help>
-
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt730</citation>
     </citations>