comparison minimap2.xml @ 10:77b2770508f6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d7c1c96bd5297839271cf69ad2129a0f47a29b89"

9:8c6cd2650d1f

<?xml version="1.0"?>
<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy2" profile="17.01">
    <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
    <macros>
        <token name="@TOOL_VERSION@">2.17</token>
        <xml name="pe_anaylsis_fixed_selector">
            <param name="analysis_type_selector" type="select"

    ## Mapping options
    #if str($mapping_options.f):
        -f $mapping_options.f
    #end if
    #if str($mapping_options.min_occ_floor):
        --min-occ-floor $min_occ_floor
    #end if
    #if str($mapping_options.g):
        -g $mapping_options.g
    #end if
    #if str($mapping_options.r):

            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
        </test>
        <test>
            <!-- test alignment options -->
            <param name="reference_source_selector" value="cached" />
            <param name="ref_file" value="bwa-mem-mt-genome"/>
            <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"/>
            <section name="alignment_options">

10:77b2770508f6

<?xml version="1.0"?>
<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy3" profile="17.01">
    <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
    <macros>
        <token name="@TOOL_VERSION@">2.17</token>
        <xml name="pe_anaylsis_fixed_selector">
            <param name="analysis_type_selector" type="select"

    ## Mapping options
    #if str($mapping_options.f):
        -f $mapping_options.f
    #end if
    #if str($mapping_options.min_occ_floor):
        --min-occ-floor $mapping_options.min_occ_floor
    #end if
    #if str($mapping_options.g):
        -g $mapping_options.g
    #end if
    #if str($mapping_options.r):

            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
        </test>
        <test>
            <!-- test alignment options -->
            <param name="reference_source_selector" value="cached" />
            <param name="min_occ_floor" value="1000"/>
            <param name="ref_file" value="bwa-mem-mt-genome"/>
            <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"/>
            <section name="alignment_options">