Mercurial > repos > iuc > minimap2
changeset 13:1f06dccdc5d1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
| author | iuc |
|---|---|
| date | Fri, 11 Jun 2021 21:40:01 +0000 |
| parents | 037c6e54df11 |
| children | 09b53c1d4ab1 |
| files | macros.xml minimap2.xml |
| diffstat | 2 files changed, 24 insertions(+), 26 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Fri May 28 21:09:55 2021 +0000 +++ b/macros.xml Fri Jun 11 21:40:01 2021 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.20</token> - <token name="@GALAXY_TOOL_VERSION@">galaxy0</token> + <token name="@GALAXY_TOOL_VERSION@">galaxy1</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0102</edam_topic> @@ -24,17 +24,15 @@ </xml> <xml name="citations"> <citations> - <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> - </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> </citations> </xml> -</macros> \ No newline at end of file +</macros>
--- a/minimap2.xml Fri May 28 21:09:55 2021 +0000 +++ b/minimap2.xml Fri Jun 11 21:40:01 2021 +0000 @@ -6,7 +6,6 @@ </macros> <expand macro="edam_ontology"/> <expand macro="requirements"/> - <expand macro="pe_anaylsis_fixed_selector"/> <stdio> <exit_code range="1:" level="fatal" /> <regex match="\[ERROR\]" source="stderr" level="fatal" /> @@ -147,15 +146,16 @@ #else if $fastq_input.fastq_input_selector == 'paired_collection': '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse' #end if + #if str($io_options.output_format) in ('BAM', 'CRAM'): + -a | samtools view --no-PG -hT reference.fa + #end if #if $io_options.output_format == 'BAM': - -a | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O $io_options.output_format -o '$alignment_output' #else if $io_options.output_format == 'CRAM': - -a | samtools sort -T "\${TMPDIR:-.}" -@\${GALAXY_SLOTS:-2} @@ -397,7 +397,7 @@ <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"/> - <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" /> + <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" /> </test> <test> <!-- test cram output --> @@ -416,7 +416,7 @@ <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"/> - <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" /> + <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" /> </test> <test> <!-- test paired input with one pair compressed --> @@ -425,7 +425,7 @@ <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"/> - <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" /> + <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" /> </test> <test> <!-- test collection input --> @@ -438,7 +438,7 @@ <element name="reverse" value="bwa-mem-fastq2.fq" /> </collection> </param> - <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="2" /> + <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" /> </test> <test> <!-- test data table reference --> @@ -447,7 +447,7 @@ <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"/> - <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" /> + <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" /> </test> <test> <!-- test alignment options --> @@ -470,7 +470,7 @@ <param name="z" value="400" /> <param name="s" value="40" /> </section> - <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" /> + <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" /> </test> <test> <!-- test paf output --> @@ -489,7 +489,7 @@ <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" /> - <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="2" /> + <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" /> </test> <test> <!-- test mask-len option --> @@ -501,7 +501,7 @@ <section name="mapping_options"> <param name="mask_len" value="100"/> </section> - <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="2" /> + <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="4" /> </test> <test> <!-- test map-hifi --> @@ -510,7 +510,7 @@ <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"/> - <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="2" /> + <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" /> </test> <test> <!-- test kmer ocurrence interval option --> @@ -524,7 +524,7 @@ <param name="lower_limit" value="10"/> <param name="upper_limit" value="30"/> </conditional> - <output name="alignment_output" ftype="bam" file="minimap2-test-kmer_ocurrence.bam" lines_diff="2" /> + <output name="alignment_output" ftype="bam" file="minimap2-test-kmer_ocurrence.bam" lines_diff="4" /> </test> </tests> <help>