--- a/rseqc_macros.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/rseqc_macros.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">5.0.1</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">5.0.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@GALAXY_VERSION@">20.01</token>
     <xml name="requirements">
         <requirements>
@@ -15,52 +15,41 @@
     </xml>
     <xml name="stdio">
         <stdio>
-            <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
-            <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
+            <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information"/>
+            <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information"/>
         </stdio>
     </xml>
-
     <!-- Params -->
     <xml name="bam_param">
         <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)"/>
     </xml>
-
     <xml name="refgene_param">
         <param argument="--refgene" type="data" format="bed12" label="Reference gene model" help="Reference gene model in BED fomat"/>
     </xml>
-
     <xml name="mapq_param">
-        <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;"/>
+        <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 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 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 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 argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50" />
+        <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50"/>
     </xml>
-
     <xml name="layout_param">
         <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)">
             <option value="SE" selected="true">Single-end</option>
             <option value="PE">Paired-end</option>
         </param>
     </xml>
-
     <xml name="strand_type_param">
         <conditional name="strand_type">
             <param name="strand_specific" type="select" label="Strand-specific?">
@@ -69,21 +58,20 @@
                 <option value="single">Single-End RNA-seq</option>
             </param>
             <when value="pair">
-                <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" help="(--strand)">
-                    <option value="sd" selected="true"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
-                    <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
+                <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --&gt; parent)" help="(--strand)">
+                    <option value="sd" selected="true"> read1 (positive --&gt; positive; negative --&gt; negative), read2 (positive --&gt; negative; negative --&gt; positive)</option>
+                    <option value="ds">read1 (positive --&gt; negative; negative --&gt; positive), read2 (positive --&gt; positive; negative --&gt; negative)</option>
                 </param>
             </when>
             <when value="single">
-                <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" help="(--strand)">
-                    <option value="s" selected="true">positive --> positive; negative --> negative</option>
-                    <option value="d">positive --> negative; negative --> positive</option>
+                <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --&gt; parent)" help="(--strand)">
+                    <option value="s" selected="true">positive --&gt; positive; negative --&gt; negative</option>
+                    <option value="d">positive --&gt; negative; negative --&gt; positive</option>
                 </param>
             </when>
-            <when value="none"></when>
+            <when value="none"/>
         </conditional>
     </xml>
-
     <xml name="multihits_param">
         <conditional name="multihits_type">
             <param name="multihits_type_selector" type="select" label="Reads with multiple hits" help="(--skip-multi-hits)">
@@ -91,34 +79,26 @@
                 <option value="skip_multihits">Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads</option>
             </param>
             <when value="skip_multihits">
-                <expand macro="mapq_param" />
+                <expand macro="mapq_param"/>
             </when>
-            <when value="use_multihits" />
+            <when value="use_multihits"/>
         </conditional>
     </xml>
-
     <xml name="rscript_output_param">
-        <param name="rscript_output" type="boolean" value="false" label="Output R-Script"
-            help="Output the R-Script used to generate the plots" />
+        <param name="rscript_output" type="boolean" value="false" label="Output R-Script" help="Output the R-Script used to generate the plots"/>
     </xml>
-
-
     <!-- Output -->
-
     <xml name="pdf_output_data" token_filename="output.pdf" token_label="${tool.name} on ${on_string}: PDF">
-        <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="@LABEL@" />
+        <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="@LABEL@"/>
     </xml>
-
     <xml name="xls_output_data" token_filename="output.xls" token_label="${tool.name} on ${on_string}: XLS">
-        <data format="tabular" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@" />
+        <data format="tabular" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@"/>
     </xml>
-
     <xml name="rscript_output_data" token_filename="output.r" token_label="${tool.name} on ${on_string}: Rscript">
         <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="@LABEL@">
             <filter>rscript_output</filter>
         </data>
     </xml>
-
     <!-- Command -->
     <token name="@MULTIHITS@"><![CDATA[
         #if str($multihits_type.multihits_type_selector) == "skip_multihits"
@@ -126,7 +106,6 @@
             --mapq=${multihits_type.mapq}
         #end if
     ]]></token>
-
     <token name="@BAM_SAM_INPUTS@"><![CDATA[
         #set $extension = str($input.ext)
         ln -s -f '${input}' 'input.${extension}' &&
@@ -134,7 +113,6 @@
             ln -s -f '${input.metadata.bam_index}' 'input.bam.bai' &&
         #end if
     ]]></token>
-
     <token name="@ABOUT@">
 
 -----
@@ -158,7 +136,6 @@
 
 
     </token>
-
     <xml name="citations">
         <citations>
             <citation type="doi">10.1093/bioinformatics/bts356</citation>