From 25200b2c00364b3d371c14cb4624b246446e548b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 11 Jul 2024 16:30:10 +0200
Subject: [PATCH] udpate qualimap (#6138)

* udpate qualimap

* Update .shed.yml
---
 tools/qualimap/.shed.yml                |  4 +++
 tools/qualimap/qualimap_bamqc.xml       | 46 ++++++++-----------------
 tools/qualimap/qualimap_counts.xml      |  4 +--
 tools/qualimap/qualimap_macros.xml      |  3 +-
 tools/qualimap/qualimap_multi_bamqc.xml | 12 +++----
 tools/qualimap/qualimap_rnaseq.xml      |  4 +--
 6 files changed, 28 insertions(+), 45 deletions(-)

diff --git a/tools/qualimap/.shed.yml b/tools/qualimap/.shed.yml
index 7f319c7b9ab..646f3f2fb66 100644
--- a/tools/qualimap/.shed.yml
+++ b/tools/qualimap/.shed.yml
@@ -2,6 +2,10 @@ name: qualimap
 owner: iuc
 remote_repository_url: "https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap"
 homepage_url: "http://qualimap.bioinfo.cipf.es/"
+long_description: |
+  Qualimap 2 is a platform-independent application written in Java and
+  R that facilitates the quality control of alignment sequencing data and its
+  derivatives like feature counts.
 categories:
 - "Sequence Analysis"
 - "Transcriptomics"
diff --git a/tools/qualimap/qualimap_bamqc.xml b/tools/qualimap/qualimap_bamqc.xml
index e68be009180..c4ee606ed97 100644
--- a/tools/qualimap/qualimap_bamqc.xml
+++ b/tools/qualimap/qualimap_bamqc.xml
@@ -1,8 +1,8 @@
-<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy3">
-    <expand macro="bio_tools"/>
+<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[
@@ -76,8 +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>
@@ -85,49 +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" />
diff --git a/tools/qualimap/qualimap_counts.xml b/tools/qualimap/qualimap_counts.xml
index 4597a39d551..c14da8e23fd 100644
--- a/tools/qualimap/qualimap_counts.xml
+++ b/tools/qualimap/qualimap_counts.xml
@@ -1,5 +1,4 @@
-<tool id="qualimap_counts" name="QualiMap Counts QC" version="@VERSION@">
-    <expand macro="bio_tools"/>
+<tool id="qualimap_counts" name="QualiMap Counts QC" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <macros>
         <import>qualimap_macros.xml</import>
         <xml name="gene_info">
@@ -25,6 +24,7 @@
             </conditional>
         </xml>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
diff --git a/tools/qualimap/qualimap_macros.xml b/tools/qualimap/qualimap_macros.xml
index b6435b2ded4..7478e658be4 100644
--- a/tools/qualimap/qualimap_macros.xml
+++ b/tools/qualimap/qualimap_macros.xml
@@ -1,5 +1,6 @@
 <macros>
-    <token name="@VERSION@">2.2.2d</token>
+    <token name="@VERSION@">2.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="requirements">
         <requirements>
diff --git a/tools/qualimap/qualimap_multi_bamqc.xml b/tools/qualimap/qualimap_multi_bamqc.xml
index de1813e9e9d..a20d588a055 100644
--- a/tools/qualimap/qualimap_multi_bamqc.xml
+++ b/tools/qualimap/qualimap_multi_bamqc.xml
@@ -1,5 +1,4 @@
-<tool id="qualimap_multi_bamqc" name="QualiMap Multi-Sample BamQC" version="@VERSION@">
-    <expand macro="bio_tools"/>
+<tool id="qualimap_multi_bamqc" name="QualiMap Multi-Sample BamQC" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <macros>
         <import>qualimap_macros.xml</import>
         <xml name="test_collection">
@@ -17,6 +16,7 @@
             </collection>
         </xml>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
@@ -83,9 +83,7 @@
             <when value="individual">
                 <repeat name="bam_qc_data" default="2" min="2"
                 title="BAM QC data to combine">
-                    <param name="bam_qc_input" type="data_collection" collection_type="list" format="txt"
-                    label="Single-sample BAM QC data"
-                    help="" />
+                    <param name="bam_qc_input" type="data_collection" format="txt" label="Single-sample BAM QC data" help="" collection_type="list" />
                     <param name="sample_name" type="text"
                     label="Name to use for this dataset"
                     help="This is the name that will be used for this dataset throughout the Qualimap report. Default: Name of the raw data collection in the history" />
@@ -98,9 +96,7 @@
                     </param>
                     <repeat name="bam_qc_data" default="1" min="1"
                     title="Data associated with this group">
-                        <param name="bam_qc_input" type="data_collection" collection_type="list" format="txt" multiple="true"
-                        label="Single-sample BAM QC data"
-                        help="" />
+                        <param name="bam_qc_input" type="data_collection" format="txt" label="Single-sample BAM QC data" help="" collection_type="list" multiple="true" />
                     </repeat>
                 </repeat>
             </when>
diff --git a/tools/qualimap/qualimap_rnaseq.xml b/tools/qualimap/qualimap_rnaseq.xml
index 2c07a50abb4..978dcce7ab0 100644
--- a/tools/qualimap/qualimap_rnaseq.xml
+++ b/tools/qualimap/qualimap_rnaseq.xml
@@ -1,8 +1,8 @@
-<tool id="qualimap_rnaseq" name="QualiMap RNA-Seq QC" version="@VERSION@+galaxy1">
-    <expand macro="bio_tools"/>
+<tool id="qualimap_rnaseq" name="QualiMap RNA-Seq QC" 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[