# HG changeset patch
# User iuc
# Date 1720708945 0
# Node ID 17b35d23731f70d7e87ae7455385eb7d082e8690
# Parent  e38af83df163fb18845f4b146c0501b15c27675c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b

diff -r e38af83df163 -r 17b35d23731f qualimap_macros.xml
--- a/qualimap_macros.xml	Mon Jan 13 13:03:39 2020 -0500
+++ b/qualimap_macros.xml	Thu Jul 11 14:42:25 2024 +0000
@@ -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>
@@ -7,7 +8,11 @@
             <yield />
         </requirements>
     </xml>
-
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">qualimap</xref>
+        </xrefs>
+    </xml>
     <xml name="version_command">
         <version_command>qualimap --help | grep 'QualiMap v.' | cut -d '.' -f 2-</version_command>
     </xml>
diff -r e38af83df163 -r 17b35d23731f qualimap_multi_bamqc.xml
--- a/qualimap_multi_bamqc.xml	Mon Jan 13 13:03:39 2020 -0500
+++ b/qualimap_multi_bamqc.xml	Thu Jul 11 14:42:25 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="qualimap_multi_bamqc" name="QualiMap Multi-Sample BamQC" version="@VERSION@">
+<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">
@@ -16,6 +16,7 @@
             </collection>
         </xml>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
@@ -82,9 +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" />
@@ -97,9 +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>