Mercurial > repos > iuc > minimap2
changeset 28:f774b65c34d0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 980f7472892817697208792e4443fa579625b696
author | iuc |
---|---|
date | Tue, 04 Feb 2025 09:15:44 +0000 |
parents | 876749149e6d |
children | |
files | macros.xml minimap2.xml test-data/minimap2-self-homology.bam test-data/minimap2-test-kmer_ocurrence.bam test-data/minimap2-test-mask_len.bam test-data/minimap2-test1-fasta.bam test-data/minimap2-test1-fasta.cram test-data/minimap2-test1.bam test-data/minimap2-test2.bam test-data/minimap2-test_hifi-2-fasta.bam test-data/minimap2-test_hifi-fasta.bam |
diffstat | 11 files changed, 23 insertions(+), 21 deletions(-) [+] |
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--- 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">
--- 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"/>