comparison minimap2.xml @ 28:f774b65c34d0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 980f7472892817697208792e4443fa579625b696

27:876749149e6d

<?xml version="1.0"?>
<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
    <xrefs>
        <xref type="bio.tools">minimap2</xref>
    </xrefs>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <stdio>
        <exit_code range="1:" level="fatal" />
        <regex match="\[ERROR\]" source="stderr" level="fatal" />
    </stdio>

    #end if
    $io_options.Y
    #if $io_options.K:
        -K $io_options.K
    #end if
    -t \${GALAXY_SLOTS:-4}
    reference.fa
    #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
        '$fastq_input.fastq_input1'
    #else if $fastq_input.fastq_input_selector == 'paired':

    #else if $io_options.output_format == 'CRAM':
        | samtools sort
        -T "\${TMPDIR:-.}"
        -@\${GALAXY_SLOTS:-2}
        -O $io_options.output_format
        $io_options.eqx
        --reference reference.fa
        --output-fmt-option no_ref
        -o '$alignment_output'
    #else:
        > '$alignment_output'

                <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
                <expand macro="pe_anaylsis_fixed_selector" />
            </when>
        </conditional>
        <section name="indexing_options" title="Indexing options">
            <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
            <param argument="-k" type="integer" min="4" max="28" optional="true"  label="K-mer size" help=""/>
            <param argument="-w" type="integer" min="1" optional="true"  label="Minimizer window size" help=""/>
            <param argument="-I" type="integer" min="1" optional="true"  label="Split index for every N input gigabases" help=""/>
        </section>
        <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False">

                <when input="io_options.output_format" value="CRAM" format="cram" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <!-- test single input -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <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="4" />
        </test>
        <test>
            <!-- test cram output -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <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"/>
            <param name="output_format" value="CRAM"/>
            <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" />
        </test>
        <test>
            <!-- test paired input -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <param name="fastq_input_selector" value="paired"/>
            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
            <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
        </test>
        <test>
            <!-- test paired input with one pair compressed -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <param name="fastq_input_selector" value="paired"/>
            <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
            <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
        </test>
        <test>
            <!-- test collection input -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <param name="fastq_input_selector" value="paired_collection"/>
            <param name="fastq_input1">

                    <element name="reverse" value="bwa-mem-fastq2.fq" />
                </collection>
            </param>
            <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" />
        </test>
        <test>
            <!-- test data table reference -->
            <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"/>
            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
        </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"/>

                a valid command line is formed for the cs option -->
                <param name="cs" value="none" />
            </section>
            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
        </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="paf" file="mini_reads.paf" />
        </test>
        <test>
            <!-- test self-homology mode -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" />
            <param name="fastq_input_selector" value="single" />
            <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
            <param name="analysis_type_selector" value="self-homology" />
            <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" />
        </test>
        <test>
            <!-- test mask-len option -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <param name="fastq_input_selector" value="single"/>
            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>

            <section name="mapping_options">
                <param name="mask_len" value="100"/>
            </section>
            <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="4" />
        </test>
        <test>
            <!-- test map-hifi -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/>
            <param name="fastq_input_selector" value="single"/>
            <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
            <param name="analysis_type_selector" value="map-hifi"/>
            <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" />
        </test>
        <test>
            <!-- test map-hifi uncompressed reference-->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa"/>
            <param name="fastq_input_selector" value="single"/>
            <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
            <param name="analysis_type_selector" value="map-hifi"/>
            <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-2-fasta.bam" lines_diff="4" />
        </test>
        <test>
            <!-- test kmer ocurrence interval option -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <param name="fastq_input_selector" value="single"/>
            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>

28:f774b65c34d0

<?xml version="1.0"?>
<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <xrefs>
        <xref type="bio.tools">minimap2</xref>
    </xrefs>
    <expand macro="requirements"/>
    <stdio>
        <exit_code range="1:" level="fatal" />
        <regex match="\[ERROR\]" source="stderr" level="fatal" />
    </stdio>

    #end if
    $io_options.Y
    #if $io_options.K:
        -K $io_options.K
    #end if
    #if $io_options.eqx:
        --eqx
    #end if
    -t \${GALAXY_SLOTS:-4}
    reference.fa
    #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
        '$fastq_input.fastq_input1'
    #else if $fastq_input.fastq_input_selector == 'paired':

    #else if $io_options.output_format == 'CRAM':
        | samtools sort
        -T "\${TMPDIR:-.}"
        -@\${GALAXY_SLOTS:-2}
        -O $io_options.output_format
        --reference reference.fa
        --output-fmt-option no_ref
        -o '$alignment_output'
    #else:
        > '$alignment_output'

                <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
                <expand macro="pe_anaylsis_fixed_selector" />
            </when>
        </conditional>
        <section name="indexing_options" title="Indexing options">
            <param argument="-H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
            <param argument="-k" type="integer" min="4" max="28" optional="true"  label="K-mer size" help=""/>
            <param argument="-w" type="integer" min="1" optional="true"  label="Minimizer window size" help=""/>
            <param argument="-I" type="integer" min="1" optional="true"  label="Split index for every N input gigabases" help=""/>
        </section>
        <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False">

                <when input="io_options.output_format" value="CRAM" format="cram" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <!-- test single input -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <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="4" />
        </test>
        <test expect_num_outputs="1">
            <!-- test cram output -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <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"/>
            <param name="output_format" value="CRAM"/>
            <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" />
        </test>
        <test expect_num_outputs="1">
            <!-- test paired input -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <param name="fastq_input_selector" value="paired"/>
            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
            <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
        </test>
        <test expect_num_outputs="1">
            <!-- test paired input with one pair compressed -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <param name="fastq_input_selector" value="paired"/>
            <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
            <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
        </test>
        <test expect_num_outputs="1">
            <!-- test collection input -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <param name="fastq_input_selector" value="paired_collection"/>
            <param name="fastq_input1">

                    <element name="reverse" value="bwa-mem-fastq2.fq" />
                </collection>
            </param>
            <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" />
        </test>
        <test expect_num_outputs="1">
            <!-- test data table reference -->
            <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"/>
            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
        </test>
        <test expect_num_outputs="1">
            <!-- 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"/>

                a valid command line is formed for the cs option -->
                <param name="cs" value="none" />
            </section>
            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
        </test>        
        <test expect_num_outputs="1">
            <!-- 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="paf" file="mini_reads.paf" />
        </test>
        <test expect_num_outputs="1">
            <!-- test self-homology mode -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" />
            <param name="fastq_input_selector" value="single" />
            <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
            <param name="analysis_type_selector" value="self-homology" />
            <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" />
        </test>
        <test expect_num_outputs="1">
            <!-- test mask-len option -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <param name="fastq_input_selector" value="single"/>
            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>

            <section name="mapping_options">
                <param name="mask_len" value="100"/>
            </section>
            <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="4" />
        </test>
        <test expect_num_outputs="1">
            <!-- test map-hifi -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/>
            <param name="fastq_input_selector" value="single"/>
            <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
            <param name="analysis_type_selector" value="map-hifi"/>
            <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" />
        </test>
        <test expect_num_outputs="1">
            <!-- test map-hifi uncompressed reference-->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa"/>
            <param name="fastq_input_selector" value="single"/>
            <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
            <param name="analysis_type_selector" value="map-hifi"/>
            <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-2-fasta.bam" lines_diff="4" />
        </test>
        <test expect_num_outputs="1">
            <!-- test kmer ocurrence interval option -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
            <param name="fastq_input_selector" value="single"/>
            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>