| Previous changeset 19:be1d967337e4 (2023-05-04) Next changeset 21:5cc34c3f440d (2024-04-03) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b |
|
modified:
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 |
| b |
| diff -r be1d967337e4 -r 92678fcb1a5f macros.xml --- a/macros.xml Thu May 04 21:55:04 2023 +0000 +++ b/macros.xml Mon Mar 18 16:43:36 2024 +0000 |
| b |
| @@ -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"> |
| b |
| diff -r be1d967337e4 -r 92678fcb1a5f minimap2.xml --- a/minimap2.xml Thu May 04 21:55:04 2023 +0000 +++ b/minimap2.xml Mon Mar 18 16:43:36 2024 +0000 |
| b |
| @@ -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"/> |
| b |
| diff -r be1d967337e4 -r 92678fcb1a5f test-data/minimap2-self-homology.bam |
| b |
| Binary file test-data/minimap2-self-homology.bam has changed |
| b |
| diff -r be1d967337e4 -r 92678fcb1a5f test-data/minimap2-test-kmer_ocurrence.bam |
| b |
| Binary file test-data/minimap2-test-kmer_ocurrence.bam has changed |
| b |
| diff -r be1d967337e4 -r 92678fcb1a5f test-data/minimap2-test-mask_len.bam |
| b |
| Binary file test-data/minimap2-test-mask_len.bam has changed |
| b |
| diff -r be1d967337e4 -r 92678fcb1a5f test-data/minimap2-test1-fasta.bam |
| b |
| Binary file test-data/minimap2-test1-fasta.bam has changed |
| b |
| diff -r be1d967337e4 -r 92678fcb1a5f test-data/minimap2-test1-fasta.cram |
| b |
| Binary file test-data/minimap2-test1-fasta.cram has changed |
| b |
| diff -r be1d967337e4 -r 92678fcb1a5f test-data/minimap2-test1.bam |
| b |
| Binary file test-data/minimap2-test1.bam has changed |
| b |
| diff -r be1d967337e4 -r 92678fcb1a5f test-data/minimap2-test2.bam |
| b |
| Binary file test-data/minimap2-test2.bam has changed |
| b |
| diff -r be1d967337e4 -r 92678fcb1a5f test-data/minimap2-test_hifi-2-fasta.bam |
| b |
| Binary file test-data/minimap2-test_hifi-2-fasta.bam has changed |
| b |
| diff -r be1d967337e4 -r 92678fcb1a5f test-data/minimap2-test_hifi-fasta.bam |
| b |
| Binary file test-data/minimap2-test_hifi-fasta.bam has changed |