--- a/rseqc_macros.xml	Sat Dec 18 19:41:19 2021 +0000
+++ b/rseqc_macros.xml	Sat Nov 26 15:19:14 2022 +0000
@@ -1,10 +1,10 @@
 <macros>
-
-    <token name="@TOOL_VERSION@">2.6.4</token>
-
+    <token name="@TOOL_VERSION@">5.0.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@GALAXY_VERSION@">20.01</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.6.4">rseqc</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">rseqc</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -22,35 +22,36 @@
 
     <!-- Params -->
     <xml name="bam_param">
-        <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/>
+        <param name="input" type="data" label="Input BAM file" format="bam" help="(--input-file)"/>
     </xml>
 
     <xml name="bam_sam_param">
-        <param name="input" type="data" label="Input .bam/.sam file" format="bam,sam" help="(--input-file)"/>
+        <param name="input" type="data" label="Input BAM/SAM file" format="bam,sam" help="(--input-file)"/>
     </xml>
 
     <xml name="refgene_param">
-        <param name="refgene" type="data" format="bed12" label="Reference gene model" help="(--refgene)"/>
+        <param argument="--refgene" type="data" format="bed12" label="Reference gene model" help="Reference gene model in BED fomat"/>
     </xml>
 
     <xml name="mapq_param">
-        <param name="mapq" type="integer" label="Minimum mapping quality" value="30" help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot; (--mapq)"/>
+        <param argument="--mapq" type="integer" label="Minimum mapping quality" value="30" 
+            help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot;"/>
     </xml>
 
     <xml name="readlength_param">
-        <param name="readlength" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length (--read-align-length)"/>
+        <param argument="--read-align-length" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length"/>
     </xml>
 
     <xml name="readnum_param">
-        <param name="readnum" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile (--read-num)"/>
+        <param argument="--read-num" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile"/>
     </xml>
 
     <xml name="sample_size_param">
-        <param name="sample_size" type="integer" label="Number of reads sampled from SAM/BAM file (default = 200000)" value="200000" min="1" help="(--sample-size)"/>
+        <param argument="--sample-size" type="integer" label="Number of reads sampled" value="200000" min="1" help="Number of reads sampled from SAM/BAM file"/>
     </xml>
 
     <xml name="min_intron_param">
-        <param name="min_intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" help="(--min-intron)" />
+        <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50" />
     </xml>
 
     <xml name="layout_param">
@@ -119,14 +120,20 @@
     </xml>
 
     <!-- Command -->
-    <token name="@MULTIHITS@">
-<![CDATA[
-#if str($multihits_type.multihits_type_selector) == "skip_multihits"
-    --skip-multi-hits
-    --mapq=${multihits_type.mapq}
-#end if
-]]>
-    </token>
+    <token name="@MULTIHITS@"><![CDATA[
+        #if str($multihits_type.multihits_type_selector) == "skip_multihits"
+            --skip-multi-hits
+            --mapq=${multihits_type.mapq}
+        #end if
+    ]]></token>
+
+    <token name="@BAM_SAM_INPUTS@"><![CDATA[
+        #set $extension = str($input.ext)
+        ln -s -f '${input}' 'input.${extension}' &&
+        #if $extension == 'bam'
+            ln -s -f '${input.metadata.bam_index}' 'input.bam.bai' &&
+        #end if
+    ]]></token>
 
     <token name="@ABOUT@">