--- a/macros.xml	Mon Jun 15 16:55:13 2020 -0400
+++ b/macros.xml	Tue Mar 23 20:23:14 2021 +0000
@@ -5,7 +5,7 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">2.29.2</token>
+    <token name="@TOOL_VERSION@">2.30.0</token>
     <token name="@SAMTOOLS_VERSION@">1.9</token>
     <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf,encodepeak</token>
     <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token>
@@ -77,6 +77,19 @@
             </when>
         </conditional>
     </xml>
+    <xml name="input_optional_genome_file">
+        <conditional name="genome">
+            <param name="genome_choose" argument="-g" type="select"
+                label="Specify a genome file that defines the expected chromosome order in the input files." >
+                <option value="" selected="true">No</option>
+                <option value="-g">Yes</option>
+            </param>
+            <when value="-g">
+                <expand macro="input_conditional_genome_file" />
+            </when>
+            <when value="" />
+        </conditional>
+    </xml>
     <token name="@GENOME_FILE@">
 #if $genome_file_opts.genome_file_opts_selector == "loc":
     '$genome_file_opts.genome.fields.len_path'
@@ -223,6 +236,23 @@
         <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
         <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
     </xml>
+    <xml name="sorted">
+        <!-- -sorted -g  -->
+        <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
+            label="For coordinate sorted input file the more efficient sweeping algorithm is enabled."/>
+    </xml>
+    <token name="@SORTED@">
+<![CDATA[
+$sorted
+#if str($sorted) != '':
+    #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
+        -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
+    #else if str($reduce_or_iterate.reduce_or_iterate_selector) == 'reduce' and str($reduce_or_iterate.inputB) != 'None' and $reduce_or_iterate.inputB[0].is_of_type('bam'):
+        -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
+    #end if
+#end if
+]]>
+    </token>
     <token name="@REFERENCES@">
 <![CDATA[
 ------