--- a/qualimap_bamqc.xml	Wed May 20 15:56:11 2020 -0400
+++ b/qualimap_bamqc.xml	Thu Jul 11 14:42:43 2024 +0000
@@ -1,7 +1,8 @@
-<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy3">
+<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <macros>
         <import>qualimap_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
@@ -75,8 +76,7 @@
         @MASSAGE_OUTPUT@
     ]]></command>
     <inputs>
-        <param argument="-bam" name="input1" type="data" format="bam"
-        label="Mapped reads input dataset" />
+        <param name="input1" argument="-bam" type="data" format="bam" label="Mapped reads input dataset" />
         <conditional name="stats_regions">
             <param name="region_select" type="select" label="Reference genome regions to calculate mapping statistics for">
                 <option value="all">All (whole genome)</option>
@@ -84,49 +84,32 @@
             </param>
             <when value="all" />
             <when value="custom_regions">
-                <param argument="-gff" name="regions" type="data" format="gff,gtf,bed"
-                label="Dataset specifying regions" />
-                <param argument="-os" name="outside_stats" type="boolean" truevalue="--outside-stats" falsevalue="" checked="false"
-                label="Invert regions"
-                help="If selected, report read statistics *outside* the regions in the regions file." />
+                <param name="regions" argument="-gff" type="data" format="gff,gtf,bed" label="Dataset specifying regions" />
+                <param name="outside_stats" argument="-os" type="boolean" truevalue="--outside-stats" falsevalue="" checked="false" label="Invert regions" help="If selected, report read statistics *outside* the regions in the regions file." />
             </when>
         </conditional>
-        <param argument="-oc" name="per_base_coverage" type="boolean" truevalue="--output-genome-coverage" falsevalue="" checked="false"
-        label="Generate per-base coverage output"
-        help="Produce additional tabular output listing the coverage at every site (omitting only zero-coverage positions) in the selected regions of the genome. Caution: Will generate a huge dataset for anything but small input genomes or restricted regions!" />
-        <param argument="--skip-dup-mode" name="duplicate_skipping" type="select" display="checkboxes" multiple="true" optional="true"
-        label="Skip duplicate reads">
+        <param name="per_base_coverage" argument="-oc" type="boolean" truevalue="--output-genome-coverage" falsevalue="" checked="false" label="Generate per-base coverage output" help="Produce additional tabular output listing the coverage at every site (omitting only zero-coverage positions) in the selected regions of the genome. Caution: Will generate a huge dataset for anything but small input genomes or restricted regions!" />
+        <param name="duplicate_skipping" argument="--skip-dup-mode" type="select" optional="true" label="Skip duplicate reads" display="checkboxes" multiple="true">
             <option value="0" selected="true">Reads flagged as duplicates in input</option>
             <option value="1">Duplicates detected by Qualimap</option>
         </param>
         <section name="plot_specific" title="Settings affecting specific plots" expanded="false">
-            <param argument="-nw" name="n_bins" type="integer" value="400"
-            label="Number of bins to use in across-reference plots"
-            help="Affected plots: Coverage, Mapping Quality and Insert Size across reference, Mapped reads GC-content distribution; the value determines the resolution of the affected plots. Note: The lower the value, the higher the memory usage of the tool!" />
-            <param argument="-c" name="paint_chromosome_limits" type="boolean" truevalue="--paint-chromosome-limits" falsevalue="" checked="true"
-            label="Draw chromosome limits"
-            help="Affected plots: Coverage, Mapping Quality and Insert Size across reference; in across-reference plots, indicate chromosome boundaries with dotted lines and labels" />
-            <param argument="-gd" name="genome_gc_distr" type="select" optional="true"
-            label="Plot expected GC-content distribution of the following reference genome"
-            help="Affected plot: Mapped reads GC-content distribution; include a precalculated GC-content distribution for the selected (Qualimap-supported) reference genome in the plot">
+            <param name="n_bins" argument="-nw" type="integer" value="400" label="Number of bins to use in across-reference plots" help="Affected plots: Coverage, Mapping Quality and Insert Size across reference, Mapped reads GC-content distribution; the value determines the resolution of the affected plots. Note: The lower the value, the higher the memory usage of the tool!" />
+            <param name="paint_chromosome_limits" argument="-c" type="boolean" truevalue="--paint-chromosome-limits" falsevalue="" checked="true" label="Draw chromosome limits" help="Affected plots: Coverage, Mapping Quality and Insert Size across reference; in across-reference plots, indicate chromosome boundaries with dotted lines and labels" />
+            <param name="genome_gc_distr" argument="-gd" type="select" optional="true" label="Plot expected GC-content distribution of the following reference genome" help="Affected plot: Mapped reads GC-content distribution; include a precalculated GC-content distribution for the selected (Qualimap-supported) reference genome in the plot">
                 <option value="hg19">Human genome (hg19)</option>
                 <option value="mm9">Mouse genome (mm9)</option>
                 <option value="mm10">Mouse genome (mm10)</option>
             </param>
-            <param argument="-hm" name="homopolymer_size" type="integer" value="3" min="2"
-            label="Homopolymer size"
-            help="Affected plot: Homopolymer indels; sets the minimal number of consecutive bases that define a homopolymer" />
+            <param name="homopolymer_size" argument="-hm" type="integer" min="2" value="3" label="Homopolymer size" help="Affected plot: Homopolymer indels; sets the minimal number of consecutive bases that define a homopolymer" />
         </section>
     </inputs>
     <outputs>
-        <data name="output_html" format="html"
-        label="${tool.name} report on ${on_string}" />
-        <data name="output_per_base_coverage" format="tsv"
-        label="${tool.name} per-base coverage on ${on_string}">
+        <data name="output_html" format="html" label="${tool.name} report on ${on_string}" />
+        <data name="output_per_base_coverage" format="tsv" label="${tool.name} per-base coverage on ${on_string}">
             <filter>per_base_coverage</filter>
         </data>
-        <collection name="raw_data" type="list"
-        label="Raw data for ${tool.name} on ${on_string}">
+        <collection name="raw_data" type="list" label="Raw data for ${tool.name} on ${on_string}">
             <data name="genome_results" format="txt" from_work_dir="results/summary_report.txt" />
             <data name="coverage_across_reference" format="tsv" from_work_dir="results/coverage_across_reference.txt" />
             <data name="coverage_histogram" format="tsv" from_work_dir="results/coverage_histogram.txt" />