# HG changeset patch
# User iuc
# Date 1761255215 0
# Node ID cbe067a674a9ff71d4b8207e526a1368c62eb36d
# Parent  f774b65c34d0a0304c77777af0df107527456cc4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 commit a02980a757cba9680a7863a3e67e9e10d77fc9f6

diff -r f774b65c34d0 -r cbe067a674a9 macros.xml
--- a/macros.xml	Tue Feb 04 09:15:44 2025 +0000
+++ b/macros.xml	Thu Oct 23 21:33:35 2025 +0000
@@ -1,6 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">2.28</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@PROFILE@">24.0</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0102</edam_topic>
@@ -26,13 +27,7 @@
         <citations>
             <citation type="doi">10.1093/bioinformatics/btp324</citation>
             <citation type="doi">10.1093/bioinformatics/btp698</citation>
-            <citation type="bibtex">@misc{1303.3997,
-                Author = {Heng Li},
-                Title = {Minimap2: fast pairwise alignment for long nucleotide sequences},
-                Year = {2017},
-                Eprint = {arXiv:1708.01492},
-                url = {https://arxiv.org/abs/1708.01492},
-                }</citation>
+            <citation type="doi">10.1093/bioinformatics/bty191</citation>
         </citations>
     </xml>
 </macros>
diff -r f774b65c34d0 -r cbe067a674a9 minimap2.xml
--- a/minimap2.xml	Tue Feb 04 09:15:44 2025 +0000
+++ b/minimap2.xml	Thu Oct 23 21:33:35 2025 +0000
@@ -1,5 +1,4 @@
-<?xml version="1.0"?>
-<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
     <macros>
         <import>macros.xml</import>
@@ -146,10 +145,8 @@
     #end if
     -t \${GALAXY_SLOTS:-4}
     reference.fa
-    #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
+    #if $fastq_input.fastq_input_selector == 'single':
         '$fastq_input.fastq_input1'
-    #else if $fastq_input.fastq_input_selector == 'paired':
-         '$fastq_input.fastq_input1' '$fastq_input.fastq_input2'
     #else if $fastq_input.fastq_input_selector == 'paired_collection':
          '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
     #end if
@@ -198,9 +195,7 @@
         <conditional name="fastq_input">
             <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
                 <option value="single">Single</option>
-                <option value="paired">Paired</option>
                 <option value="paired_collection">Paired Collection</option>
-                <option value="paired_iv">Paired Interleaved</option>
             </param>
             <!-- below, preset options are only offered for single-end input
             because paired-end alignment in minimap2 is only enabled with -x sr
@@ -224,19 +219,10 @@
                     <option value="self-homology">Construct a self-homology map - use same genome as query and reference (-DP -k19 -w19 -m200) (self-homology)</option>
                 </param>
             </when>
-            <when value="paired">
-                <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
-                <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
-                <expand macro="pe_anaylsis_fixed_selector" />
-            </when>
             <when value="paired_collection">
                 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
                 <expand macro="pe_anaylsis_fixed_selector" />
             </when>
-            <when value="paired_iv">
-                <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
-                <expand macro="pe_anaylsis_fixed_selector" />
-            </when>
         </conditional>
         <section name="indexing_options" title="Indexing options">
             <param argument="-H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
@@ -401,71 +387,94 @@
     <tests>
         <test expect_num_outputs="1">
             <!-- test single input -->
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="single"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
-            <param name="analysis_type_selector" value="sr"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="single"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
+                <param name="analysis_type_selector" value="sr"/>
+            </conditional>
             <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
         </test>
         <test expect_num_outputs="1">
             <!-- test cram output -->
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="single"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
-            <param name="analysis_type_selector" value="sr"/>
-            <param name="output_format" value="CRAM"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="single"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
+                <param name="analysis_type_selector" value="sr"/>
+            </conditional>
+            <section name="io_options">
+                <param name="output_format" value="CRAM"/>
+            </section>
             <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" />
         </test>
         <test expect_num_outputs="1">
             <!-- test paired input -->
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="paired"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
-            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="paired_collection"/>
+                <param name="fastq_input1">
+                    <collection type="paired">
+                        <element name="forward" value="bwa-mem-fastq1.fq" />
+                        <element name="reverse" value="bwa-mem-fastq2.fq" />
+                    </collection>
+                </param>
+            </conditional>
             <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
         </test>
         <test expect_num_outputs="1">
             <!-- test paired input with one pair compressed -->
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="paired"/>
-            <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
-            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="paired_collection"/>
+                <param name="fastq_input1">
+                    <collection type="paired">
+                        <element name="forward" value="bwa-mem-fastq1.fq.gz" />
+                        <element name="reverse" value="bwa-mem-fastq2.fq" />
+                    </collection>
+                </param>
+            </conditional>
             <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
         </test>
         <test expect_num_outputs="1">
-            <!-- test collection input -->
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="paired_collection"/>
-            <param name="fastq_input1">
-                <collection type="paired">
-                    <element name="forward" value="bwa-mem-fastq1.fq" />
-                    <element name="reverse" value="bwa-mem-fastq2.fq" />
-                </collection>
-            </param>
-            <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" />
-        </test>
-        <test expect_num_outputs="1">
             <!-- test data table reference -->
-            <param name="reference_source_selector" value="cached" />
-            <param name="ref_file" value="bwa-mem-mt-genome"/>
-            <param name="fastq_input_selector" value="single"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
-            <param name="analysis_type_selector" value="sr"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached" />
+                <param name="ref_file" value="bwa-mem-mt-genome"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="single"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
+                <param name="analysis_type_selector" value="sr"/>
+            </conditional>
             <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
         </test>
         <test expect_num_outputs="1">
             <!-- test alignment options -->
-            <param name="reference_source_selector" value="cached" />
-            <param name="min_occ_floor" value="1000"/>
-            <param name="ref_file" value="bwa-mem-mt-genome"/>
-            <param name="fastq_input_selector" value="single"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
-            <param name="analysis_type_selector" value="sr"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached" />
+                <param name="ref_file" value="bwa-mem-mt-genome"/>
+            </conditional>
+            <section name="mapping_options">
+                <param name="min_occ_floor" value="1000"/>
+            </section>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="single"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
+                <param name="analysis_type_selector" value="sr"/>
+            </conditional>
             <section name="alignment_options">
                 <!-- the folowing settings correspond to the defaults for "sr"
                 mode. The purpose is to check that all alignment params get
@@ -488,30 +497,44 @@
         </test>        
         <test expect_num_outputs="1">
             <!-- test paf output -->
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fastqsanger"  value="mini_reads.fq" />
-            <param name="fastq_input_selector" value="single"/>
-            <param name="fastq_input1" ftype="fastqsanger"  value="mini_reads.fq" />
-            <param name="analysis_type_selector" value="ava-ont"/>
-            <param name="output_format" value="paf"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fastqsanger"  value="mini_reads.fq" />
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="single"/>
+                <param name="fastq_input1" ftype="fastqsanger"  value="mini_reads.fq" />
+                <param name="analysis_type_selector" value="ava-ont"/>
+            </conditional>
+            <section name="io_options">
+                <param name="output_format" value="paf"/>
+            </section>
             <output name="alignment_output" ftype="paf" file="mini_reads.paf" />
         </test>
         <test expect_num_outputs="1">
             <!-- test self-homology mode -->
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" />
-            <param name="fastq_input_selector" value="single" />
-            <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
-            <param name="analysis_type_selector" value="self-homology" />
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" />
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="single" />
+                <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
+                <param name="analysis_type_selector" value="self-homology" />
+            </conditional>
             <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" />
         </test>
         <test expect_num_outputs="1">
             <!-- test mask-len option -->
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="single"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
-            <param name="analysis_type_selector" value="sr"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="single"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
+                <param name="analysis_type_selector" value="sr"/>
+            </conditional>
             <section name="mapping_options">
                 <param name="mask_len" value="100"/>
             </section>
@@ -519,40 +542,54 @@
         </test>
         <test expect_num_outputs="1">
             <!-- test map-hifi -->
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/>
-            <param name="fastq_input_selector" value="single"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
-            <param name="analysis_type_selector" value="map-hifi"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="single"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
+                <param name="analysis_type_selector" value="map-hifi"/>
+            </conditional>
             <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" />
         </test>
         <test expect_num_outputs="1">
             <!-- test map-hifi uncompressed reference-->
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa"/>
-            <param name="fastq_input_selector" value="single"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
-            <param name="analysis_type_selector" value="map-hifi"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="single"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
+                <param name="analysis_type_selector" value="map-hifi"/>
+            </conditional>
             <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-2-fasta.bam" lines_diff="4" />
         </test>
         <test expect_num_outputs="1">
             <!-- test kmer ocurrence interval option -->
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="single"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
-            <param name="analysis_type_selector" value="sr"/>
-            <conditional name="kmer_ocurrence_interval">
-                <param name="interval" value="enabled"/>
-                <param name="lower_limit" value="10"/>
-                <param name="upper_limit" value="30"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
             </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="single"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
+                <param name="analysis_type_selector" value="sr"/>
+            </conditional>
+            <section name="mapping_options">
+                <conditional name="kmer_ocurrence_interval">
+                    <param name="interval" value="enabled"/>
+                    <param name="lower_limit" value="10"/>
+                    <param name="upper_limit" value="30"/>
+                </conditional>
+            </section>
             <output name="alignment_output" ftype="bam" file="minimap2-test-kmer_ocurrence.bam" lines_diff="4" />
         </test>
     </tests>
     <help>
 
-Users’ Guide
+Users' Guide
 ------------
 
 Minimap2 is a versatile sequence alignment program that aligns DNA or