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comparison minimap2.xml @ 17:f25bf202bc17 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d7c1c96bd5297839271cf69ad2129a0f47a29b89"
author iuc
date Thu, 11 Feb 2021 19:10:13 +0000
parents fd3673a18ad3
children 0969cc2ddf5f
comparison
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16:fd3673a18ad3 17:f25bf202bc17
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">