--- a/crossmap_bed.xml	Thu Jul 15 16:19:05 2021 +0000
+++ b/crossmap_bed.xml	Thu Jan 20 04:31:56 2022 +0000
@@ -18,15 +18,15 @@
     <command><![CDATA[
 CrossMap.py bed
 '${chain_source.input_chain}'
-
 '${input}'
 
 #if $merge_unmapped_entries:
     > '${output_combined}'
 #else:
     output
+    --unmap-file output.unmap
 #end if
-
+--chromid $chromid
     ]]></command>
 
 
@@ -35,7 +35,11 @@
                help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
 
         <expand macro="chain" />
-
+        <param name="chromid" type="select" label="Style of chromosome IDs">
+            <option value="a" selected="true">As-is</option>
+            <option value="l">Long style, e.g. chr1, chrX</option>
+            <option value="s">Short style, e.g. 1, X</option>
+        </param>
         <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/>
     </inputs>
 
@@ -76,6 +80,7 @@
             <param name="index_source" value="history"/>
             <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
             <param name="merge_unmapped_entries" value="false" />
+            <param name="chromid" value="s" />
 
             <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/>
             <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/>
@@ -85,6 +90,7 @@
             <param name="index_source" value="history"/>
             <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
             <param name="merge_unmapped_entries" value="true" />
+            <param name="chromid" value="s" />
 
             <output name="output_combined" file="test_bed_02_output_a__all.bed"/>
         </test>