--- a/crossmap_bam.xml	Thu May 24 19:09:17 2018 -0400
+++ b/crossmap_bam.xml	Wed Sep 11 19:26:44 2019 -0400
@@ -7,6 +7,9 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
+
+ln -s '${input}' ./input.bam &&
+
 CrossMap.py bam
 '${chain_source.input_chain}'
 $optional_tags
@@ -15,7 +18,7 @@
 -s $insert_size_stdev
 -t $insert_size_fold
 
-'${input}'
+./input.bam
 output
     ]]></command>
     <inputs>
@@ -27,7 +30,8 @@
 
         <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/>
         <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/>
-        <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/>
+        <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange"
+            help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/>
     </inputs>
 
     <outputs>