Mercurial > repos > iuc > minimap2
comparison minimap2.xml @ 10:77b2770508f6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d7c1c96bd5297839271cf69ad2129a0f47a29b89"
author | iuc |
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date | Thu, 11 Feb 2021 19:10:41 +0000 |
parents | 8c6cd2650d1f |
children | f54f5baedfdd |
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9:8c6cd2650d1f | 10:77b2770508f6 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy2" profile="17.01"> | 2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy3" profile="17.01"> |
3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description> | 3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description> |
4 <macros> | 4 <macros> |
5 <token name="@TOOL_VERSION@">2.17</token> | 5 <token name="@TOOL_VERSION@">2.17</token> |
6 <xml name="pe_anaylsis_fixed_selector"> | 6 <xml name="pe_anaylsis_fixed_selector"> |
7 <param name="analysis_type_selector" type="select" | 7 <param name="analysis_type_selector" type="select" |
49 ## Mapping options | 49 ## Mapping options |
50 #if str($mapping_options.f): | 50 #if str($mapping_options.f): |
51 -f $mapping_options.f | 51 -f $mapping_options.f |
52 #end if | 52 #end if |
53 #if str($mapping_options.min_occ_floor): | 53 #if str($mapping_options.min_occ_floor): |
54 --min-occ-floor $min_occ_floor | 54 --min-occ-floor $mapping_options.min_occ_floor |
55 #end if | 55 #end if |
56 #if str($mapping_options.g): | 56 #if str($mapping_options.g): |
57 -g $mapping_options.g | 57 -g $mapping_options.g |
58 #end if | 58 #end if |
59 #if str($mapping_options.r): | 59 #if str($mapping_options.r): |
438 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" /> | 438 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" /> |
439 </test> | 439 </test> |
440 <test> | 440 <test> |
441 <!-- test alignment options --> | 441 <!-- test alignment options --> |
442 <param name="reference_source_selector" value="cached" /> | 442 <param name="reference_source_selector" value="cached" /> |
443 <param name="min_occ_floor" value="1000"/> | |
443 <param name="ref_file" value="bwa-mem-mt-genome"/> | 444 <param name="ref_file" value="bwa-mem-mt-genome"/> |
444 <param name="fastq_input_selector" value="single"/> | 445 <param name="fastq_input_selector" value="single"/> |
445 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> | 446 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> |
446 <param name="analysis_type_selector" value="sr"/> | 447 <param name="analysis_type_selector" value="sr"/> |
447 <section name="alignment_options"> | 448 <section name="alignment_options"> |