comparison minimap2.xml @ 3:1650a97189be draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 1672eb3642d19c8502322115b86846297cd5a6b0

2:4070f129540a

<?xml version="1.0"?>
<tool id="minimap2" name="Map with minimap2" version="2.4.1" profile="17.01">
    <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
    <requirements>
        <requirement type="package" version="2.4">minimap2</requirement>
        <requirement type="package" version="1.6">samtools</requirement>
    </requirements>
    <version_command>minimap2 --version</version_command>
    <command>
<![CDATA[

    $io_options.Q
    $io_options.L
    #if $io_options.cs:
        --cs $io_options.cs
    #end if
    #if $io_options.K:
        -K $io_options.K
    #end if
    -t \${GALAXY_SLOTS:-4}
    reference.fa

            <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below.">
                <option value="none">no</option>
                <option value="short">short</option>
                <option value="long">long</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)">
            <actions>

3:1650a97189be

<?xml version="1.0"?>
<tool id="minimap2" name="Map with minimap2" version="2.5" profile="17.01">
    <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
    <requirements>
        <requirement type="package" version="2.5">minimap2</requirement>
        <requirement type="package" version="1.6">samtools</requirement>
    </requirements>
    <version_command>minimap2 --version</version_command>
    <command>
<![CDATA[

    $io_options.Q
    $io_options.L
    #if $io_options.cs:
        --cs $io_options.cs
    #end if
    $io_options.Y
    #if $io_options.K:
        -K $io_options.K
    #end if
    -t \${GALAXY_SLOTS:-4}
    reference.fa

            <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below.">
                <option value="none">no</option>
                <option value="short">short</option>
                <option value="long">long</option>
            </param>
            <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="use soft clipping for supplementary alignments ?"/>
        </section>
    </inputs>
    <outputs>
        <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)">
            <actions>