Updated Minimap2 tool, debugged linting errors (#5889)

* Updating tools/minimap2 from version 2.26 to 2.27 * Resolved linting error and updated test data --------- Co-authored-by: planemo-autoupdate <[email protected]>
galaxyproject · Mar 18, 2024 · 20bce2a · 20bce2a
1 parent ae898f7
commit 20bce2a
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Showing 11 changed files with 19 additions and 19 deletions.
diff --git a/tools/minimap2/macros.xml b/tools/minimap2/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.26</token>
+    <token name="@TOOL_VERSION@">2.27</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
@@ -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 --git a/tools/minimap2/minimap2.xml b/tools/minimap2/minimap2.xml
@@ -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" />
@@ -237,7 +237,7 @@
             </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 +397,7 @@
         </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 +406,7 @@
             <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 +416,7 @@
             <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 +425,7 @@
             <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 +434,7 @@
             <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 +447,7 @@
             </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 +456,7 @@
             <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 +484,7 @@
             </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 +494,7 @@
             <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 +503,7 @@
             <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 +515,7 @@
             </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 +524,7 @@
             <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 +533,7 @@
             <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 --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-test2.bam b/tools/minimap2/test-data/minimap2-test2.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