comparison minimap2.xml @ 23:a9c0055e479a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9"

22:b81d44caa1a0

<?xml version="1.0"?>
<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
    <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
    <xrefs>
        <xref type="bio.tools">minimap2</xref>
    </xrefs>
    <macros>

                        </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" 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>
        <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="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 kmer ocurrence interval option -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>

23:a9c0055e479a

<?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>

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

            <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="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"/>