# HG changeset patch
# User iuc
# Date 1738660544 0
# Node ID f774b65c34d0a0304c77777af0df107527456cc4
# Parent  876749149e6d4ad3561341972e750ac64209a8d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 980f7472892817697208792e4443fa579625b696

diff -r 876749149e6d -r f774b65c34d0 macros.xml
--- a/macros.xml	Thu May 04 21:54:47 2023 +0000
+++ b/macros.xml	Tue Feb 04 09:15:44 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.26</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@TOOL_VERSION@">2.28</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0102</edam_topic>
@@ -12,7 +12,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">minimap2</requirement>
-            <requirement type="package" version="1.17">samtools</requirement>
+            <requirement type="package" version="1.19.2">samtools</requirement>
         </requirements>
     </xml>
     <xml name="pe_anaylsis_fixed_selector">
diff -r 876749149e6d -r f774b65c34d0 minimap2.xml
--- a/minimap2.xml	Thu May 04 21:54:47 2023 +0000
+++ b/minimap2.xml	Tue Feb 04 09:15:44 2025 +0000
@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
-    <xrefs>
-        <xref type="bio.tools">minimap2</xref>
-    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="edam_ontology"/>
+    <xrefs>
+        <xref type="bio.tools">minimap2</xref>
+    </xrefs>
     <expand macro="requirements"/>
     <stdio>
         <exit_code range="1:" level="fatal" />
@@ -141,6 +141,9 @@
     #if $io_options.K:
         -K $io_options.K
     #end if
+    #if $io_options.eqx:
+        --eqx
+    #end if
     -t \${GALAXY_SLOTS:-4}
     reference.fa
     #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
@@ -164,7 +167,6 @@
         -T "\${TMPDIR:-.}"
         -@\${GALAXY_SLOTS:-2}
         -O $io_options.output_format
-        $io_options.eqx
         --reference reference.fa
         --output-fmt-option no_ref
         -o '$alignment_output'
@@ -237,7 +239,7 @@
             </when>
         </conditional>
         <section name="indexing_options" title="Indexing options">
-            <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
+            <param argument="-H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
             <param argument="-k" type="integer" min="4" max="28" optional="true"  label="K-mer size" help=""/>
             <param argument="-w" type="integer" min="1" optional="true"  label="Minimizer window size" help=""/>
             <param argument="-I" type="integer" min="1" optional="true"  label="Split index for every N input gigabases" help=""/>
@@ -397,7 +399,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <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"/>
@@ -406,7 +408,7 @@
             <param name="analysis_type_selector" value="sr"/>
             <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
         </test>
-        <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"/>
@@ -416,7 +418,7 @@
             <param name="output_format" value="CRAM"/>
             <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" />
         </test>
-        <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"/>
@@ -425,7 +427,7 @@
             <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
             <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
         </test>
-        <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"/>
@@ -434,7 +436,7 @@
             <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
             <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
         </test>
-        <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"/>
@@ -447,7 +449,7 @@
             </param>
             <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" />
         </test>
-        <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"/>
@@ -456,7 +458,7 @@
             <param name="analysis_type_selector" value="sr"/>
             <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test alignment options -->
             <param name="reference_source_selector" value="cached" />
             <param name="min_occ_floor" value="1000"/>
@@ -484,7 +486,7 @@
             </section>
             <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
         </test>        
-        <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" />
@@ -494,7 +496,7 @@
             <param name="output_format" value="paf"/>
             <output name="alignment_output" ftype="paf" file="mini_reads.paf" />
         </test>
-        <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" />
@@ -503,7 +505,7 @@
             <param name="analysis_type_selector" value="self-homology" />
             <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" />
         </test>
-        <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"/>
@@ -515,7 +517,7 @@
             </section>
             <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="4" />
         </test>
-        <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"/>
@@ -524,7 +526,7 @@
             <param name="analysis_type_selector" value="map-hifi"/>
             <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" />
         </test>
-        <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"/>
@@ -533,7 +535,7 @@
             <param name="analysis_type_selector" value="map-hifi"/>
             <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-2-fasta.bam" lines_diff="4" />
         </test>
-        <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"/>
diff -r 876749149e6d -r f774b65c34d0 test-data/minimap2-self-homology.bam
Binary file test-data/minimap2-self-homology.bam has changed
diff -r 876749149e6d -r f774b65c34d0 test-data/minimap2-test-kmer_ocurrence.bam
Binary file test-data/minimap2-test-kmer_ocurrence.bam has changed
diff -r 876749149e6d -r f774b65c34d0 test-data/minimap2-test-mask_len.bam
Binary file test-data/minimap2-test-mask_len.bam has changed
diff -r 876749149e6d -r f774b65c34d0 test-data/minimap2-test1-fasta.bam
Binary file test-data/minimap2-test1-fasta.bam has changed
diff -r 876749149e6d -r f774b65c34d0 test-data/minimap2-test1-fasta.cram
Binary file test-data/minimap2-test1-fasta.cram has changed
diff -r 876749149e6d -r f774b65c34d0 test-data/minimap2-test1.bam
Binary file test-data/minimap2-test1.bam has changed
diff -r 876749149e6d -r f774b65c34d0 test-data/minimap2-test2.bam
Binary file test-data/minimap2-test2.bam has changed
diff -r 876749149e6d -r f774b65c34d0 test-data/minimap2-test_hifi-2-fasta.bam
Binary file test-data/minimap2-test_hifi-2-fasta.bam has changed
diff -r 876749149e6d -r f774b65c34d0 test-data/minimap2-test_hifi-fasta.bam
Binary file test-data/minimap2-test_hifi-fasta.bam has changed