--- a/crossmap_region.xml	Thu Jan 20 04:31:00 2022 +0000
+++ b/crossmap_region.xml	Mon Sep 02 12:01:39 2024 +0000
@@ -7,7 +7,7 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-CrossMap.py region
+CrossMap region
     '${chain_source.input_chain}'
     '${input}'
     $output
@@ -15,9 +15,8 @@
     --ratio $ratio
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="bed" label="BED file"
-               help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
-        <expand macro="chain" />
+        <param name="input" type="data" format="bed" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
+        <expand macro="chain"/>
         <param argument="--ratio" type="float" min="0" max="1" value="0.85" label="Minimum ratio of bases that must remap."/>
         <param argument="--chromid" type="select" label="Chromid" help="The style of chromosome IDs">
             <option value="a" selected="true">Default (a)</option>
@@ -78,7 +77,6 @@
 7. If input region cannot be consecutively mapped target assembly, it will be split.
 8. \*.unmap file contains regions that cannot be unambiguously converted.
     ]]></help>
-
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt730</citation>
     </citations>