comparison minimap2.xml @ 4:6f50f36e4481 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7

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>

    #if $reference_source.reference_source_selector == 'history':
        ln -f -s '$reference_source.ref_file' reference.fa &&
    #else:
        ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
    #end if
    minimap2 -a
    -x $analysis_type_selector
    ## indexing options
    #if $indexing_options.k:
        -k $indexing_options.k
    #end if

    #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
        '$fastq_input.fastq_input1'
    #else if $fastq_input.fastq_input_selector == 'paired':
         '$fastq_input.fastq_input1' '$fastq_input.fastq_input2'
    #else if $fastq_input.fastq_input_selector == 'paired_collection':
        '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
    #end if
    | samtools sort
    -@\${GALAXY_SLOTS:-2}
    -O $io_options.output_format
    #if $io_options.output_format == 'CRAM':
        --reference reference.fa
        --output-fmt-option no_ref
    #end if
    -o '$alignment_output'
]]>
    </command>
    <inputs>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
                <option value="cached">Use a built-in genome index</option>
                <option value="history">Use a genome from history and build index</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">

                    </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
            </when>
        </conditional>
        <section name="indexing_options" title="Indexing options">
            <!-- Homopolymer setting seems to not properly overwrite sr preset
            <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>

                <option value="f">transcript strand</option>
                <option value="b">both strands</option>
            </param>
        </section>
        <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False">
            <param name="output_format" type="select" label="Produce BAM or CRAM file?">
                <option value="BAM">BAM</option>
                <option value="CRAM">CRAM</option>
            </param>
            <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" optional="true" label="don't output base quality"/>
            <param argument="-L" type="boolean" truevalue="-L" falsevalue="" optional="true" label="write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/>
            <param argument="-K" type="integer" optional="true" label="minibatch size for mapping (in megabyte)" help="default=500M"/>
            <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.">

                        </action>
                    </when>
                </conditional>
            </actions>
            <change_format>
                <when input="io_options.output_format" value="CRAM" format="cram" />
            </change_format>
        </data>
    </outputs>
    <tests>

            <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"/>
            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
        </test>
    </tests>
    <help>

Users’ Guide

4:6f50f36e4481

<?xml version="1.0"?>
<tool id="minimap2" name="Map with minimap2" version="2.5+gx1" 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>

    #if $reference_source.reference_source_selector == 'history':
        ln -f -s '$reference_source.ref_file' reference.fa &&
    #else:
        ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
    #end if
    minimap2
    -x $analysis_type_selector
    ## indexing options
    #if $indexing_options.k:
        -k $indexing_options.k
    #end if

    #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
        '$fastq_input.fastq_input1'
    #else if $fastq_input.fastq_input_selector == 'paired':
         '$fastq_input.fastq_input1' '$fastq_input.fastq_input2'
    #else if $fastq_input.fastq_input_selector == 'paired_collection':
         '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
    #end if
    #if $io_options.output_format == 'BAM':
        -a
        | samtools sort
        -@\${GALAXY_SLOTS:-2}
        -O $io_options.output_format
        -o '$alignment_output'
    #else if $io_options.output_format == 'CRAM':
        -a
        | samtools sort
        -@\${GALAXY_SLOTS:-2}
        -O $io_options.output_format
        --reference reference.fa
        --output-fmt-option no_ref
        -o '$alignment_output'
    #end if
    > '$alignment_output'
]]>
    </command>
    <inputs>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
                <option value="cached">Use a built-in genome index</option>
                <option value="history">Use a genome from history and build index</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">

                    </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
            </when>
        </conditional>
        <section name="indexing_options" title="Indexing options">
            <!-- Homopolymer setting seems to not properly overwrite sr preset
            <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>

                <option value="f">transcript strand</option>
                <option value="b">both strands</option>
            </param>
        </section>
        <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False">
            <param name="output_format" type="select" label="Select an output format">
                <option value="BAM">BAM</option>
                <option value="CRAM">CRAM</option>
                <option value="paf">paf</option>
            </param>
            <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" optional="true" label="don't output base quality"/>
            <param argument="-L" type="boolean" truevalue="-L" falsevalue="" optional="true" label="write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/>
            <param argument="-K" type="integer" optional="true" label="minibatch size for mapping (in megabyte)" help="default=500M"/>
            <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.">

                        </action>
                    </when>
                </conditional>
            </actions>
            <change_format>
                <when input="io_options.output_format" value="paf" format="tabular" />
                <when input="io_options.output_format" value="CRAM" format="cram" />
            </change_format>
        </data>
    </outputs>
    <tests>

            <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"/>
            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
        </test>
        <test>
            <!-- test paf output -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fastqsanger"  value="mini_reads.fq" />
            <param name="fastq_input_selector" value="single"/>
            <param name="fastq_input1" ftype="fastqsanger"  value="mini_reads.fq" />
            <param name="analysis_type_selector" value="ava-ont"/>
            <param name="output_format" value="paf"/>
            <output name="alignment_output" ftype="tabular" file="mini_reads.paf" />
        </test>
    </tests>
    <help>

Users’ Guide