galaxyproject · bgruening · Oct 25, 2025 · Oct 26, 2025 · Oct 26, 2025
diff --git a/tools/minimap2/macros.xml b/tools/minimap2/macros.xml
@@ -1,7 +1,7 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.28</token>
-    <token name="@VERSION_SUFFIX@">2</token>
-    <token name="@PROFILE@">24.0</token>
+    <token name="@TOOL_VERSION@">2.30</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">24.1</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0102</edam_topic>
@@ -13,21 +13,20 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">minimap2</requirement>
-            <requirement type="package" version="1.19.2">samtools</requirement>
+            <requirement type="package" version="1.22.1">samtools</requirement>
         </requirements>
     </xml>
     <xml name="pe_anaylsis_fixed_selector">
         <param name="analysis_type_selector" type="select"
         label="Presets for PE reads alignment"
         help="These are the minimap2 preset options for PE alignment of short reads. You can customize these and other settings in the indexing, mapping and alignment options sections below.">
-            <option value="sr">Short reads without splicing (-k21 -w11 --sr -F800 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no) (sr)</option>
+            <option value="sr">Short reads without splicing (-k21 -w11 --sr --frag=yes -F800 -A2 -B8 -O12,32 -E2,1 -r100 -p.5 -N20 -f1000,5000 -n2 -m25 -s40 -g100 -2K50m --heap-sort=yes --secondary=no) (sr)</option>
         </param>
     </xml>
     <xml name="citations">
         <citations>
-            <citation type="doi">10.1093/bioinformatics/btp324</citation>
-            <citation type="doi">10.1093/bioinformatics/btp698</citation>
             <citation type="doi">10.1093/bioinformatics/bty191</citation>
+            <citation type="doi">10.1093/bioinformatics/btp352</citation>
         </citations>
     </xml>
 </macros>
diff --git a/tools/minimap2/minimap2.xml b/tools/minimap2/minimap2.xml
diff --git a/tools/minimap2/test-data/minimap2-self-homology.bam b/tools/minimap2/test-data/minimap2-self-homology.bam
diff --git a/tools/minimap2/test-data/minimap2-test-kmer_ocurrence.bam b/tools/minimap2/test-data/minimap2-test-kmer_ocurrence.bam
diff --git a/tools/minimap2/test-data/minimap2-test-mask_len.bam b/tools/minimap2/test-data/minimap2-test-mask_len.bam
diff --git a/tools/minimap2/test-data/minimap2-test1-fasta.bam b/tools/minimap2/test-data/minimap2-test1-fasta.bam
diff --git a/tools/minimap2/test-data/minimap2-test1-fasta.cram b/tools/minimap2/test-data/minimap2-test1-fasta.cram
diff --git a/tools/minimap2/test-data/minimap2-test1.bam b/tools/minimap2/test-data/minimap2-test1.bam
diff --git a/tools/minimap2/test-data/minimap2-test_hifi-2-fasta.bam b/tools/minimap2/test-data/minimap2-test_hifi-2-fasta.bam
diff --git a/tools/minimap2/test-data/minimap2-test_hifi-fasta.bam b/tools/minimap2/test-data/minimap2-test_hifi-fasta.bam