comparison winnowmap.xml @ 2:35ea4a8b1ea6 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f12e139eb362fea66360aefbbc678197e2440139"

1:44231ef8167a

<tool id="winnowmap" name="Winnowmap" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>a mapping tool optimized for repetitive sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>

         '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
    #end if
    #if $io_options.output_format == 'BAM':
        -a
        | samtools sort
        -@\${GALAXY_SLOTS:-2}
        -T "\${TMPDIR:-.}"
        -O $io_options.output_format
        -o '$alignment_output'
    #else if $io_options.output_format == 'CRAM':
        -a
        | samtools sort
        -T "\${TMPDIR:-.}"
        -@\${GALAXY_SLOTS:-2}
        -O $io_options.output_format
        $io_options.eqx
        --reference reference.fa

            <param argument="-k" type="integer" min="4" max="28" optional="true"  label="K-mer size" help="k-mer size (no larger than 28). "/>
            <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, --sv-off and --min-occ-floor options." expanded="False">
            <param name="sv_off" argument="--sv-off" type="boolean" truevalue="--sv-off" falsevalue=""  checked="False" label="Turn off SV-aware mode" help="SV aware k-mer search allows to find approximate mapping locations for a read"/>
            <param argument="-F" type="integer" min="0" value="" optional="true"
            label="Max fragment length for PE alignment"
            help="The maximum apparent fragment length up to which paired-end reads are aligned together; at higher fragment lengths the mates will be aligned independent of each other; effective only for paired-end data and when spliced alignment mode is turned off; default=800" />
            <param argument="-f" type="float" value="" optional="true" label="Filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/>
            <param argument="--min-occ-floor" name="min_occ_floor" type="integer" label="Force winnowmap to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" />

                        </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="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="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
            <param name="analysis_type_selector" value="map-ont"/>
            <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" />
        </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="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
            <param name="analysis_type_selector" value="map-ont"/>
            <param name="output_format" value="CRAM"/>
            <output name="alignment_output" ftype="cram" file="winnowmap-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"/>

                    <element name="forward" value="bwa-mem-fastq1.fq" />
                    <element name="reverse" value="bwa-mem-fastq2.fq" />
                </collection>
            </param>
            <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
            <output name="alignment_output" ftype="bam" file="winnowmap-test2.bam" lines_diff="2" />
        </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="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
            <param name="analysis_type_selector" value="map-ont"/>
            <output name="alignment_output" ftype="bam" file="winnowmap-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="E2" value="1" />
                <param name="z" value="400" />
                <param name="s" value="40" />
            </section>
            <output name="alignment_output" ftype="bam" file="winnowmap-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="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
            <param name="analysis_type_selector" value="map-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="winnowmap-self-homology.fasta" />

2:35ea4a8b1ea6

<tool id="winnowmap" name="Winnowmap" version="@TOOL_VERSION@+galaxy1" profile="20.05">
    <description>a mapping tool optimized for repetitive sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>

         '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
    #end if
    #if $io_options.output_format == 'BAM':
        -a
        | samtools sort
        --no-PG
        -@\${GALAXY_SLOTS:-2}
        -T "\${TMPDIR:-.}"
        -O $io_options.output_format
        -o '$alignment_output'
    #else if $io_options.output_format == 'CRAM':
        -a
        | samtools sort
        --no-PG
        -T "\${TMPDIR:-.}"
        -@\${GALAXY_SLOTS:-2}
        -O $io_options.output_format
        $io_options.eqx
        --reference reference.fa

            <param argument="-k" type="integer" min="4" max="28" optional="true"  label="K-mer size" help="k-mer size (no larger than 28). "/>
            <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, --sv-off and --min-occ-floor options." expanded="False">
            <param argument="--sv-off" type="boolean" truevalue="--sv-off" falsevalue=""  checked="False" label="Turn off SV-aware mode" help="SV aware k-mer search allows to find approximate mapping locations for a read"/>
            <param argument="-F" type="integer" min="0" value="" optional="true"
            label="Max fragment length for PE alignment"
            help="The maximum apparent fragment length up to which paired-end reads are aligned together; at higher fragment lengths the mates will be aligned independent of each other; effective only for paired-end data and when spliced alignment mode is turned off; default=800" />
            <param argument="-f" type="float" value="" optional="true" label="Filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/>
            <param argument="--min-occ-floor" name="min_occ_floor" type="integer" label="Force winnowmap to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" />

                        </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="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="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
            <param name="analysis_type_selector" value="map-ont"/>
            <param name="min_occ_floor" value="1000"/>
            <section name="alignment_options">
                <param name="min_occ_floor" value="1000"/>
                <param name="A" value="2"/>
                <param name="B" value="8"/>
                <param name="O" value="12"/>
                <param name="O2" value="32"/>
                <param name="E" value="2"/>
                <param name="E2" value="1"/>
                <param name="z" value="400"/>
                <param name="s" value="40"/>
            </section>
            <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" >
                <metadata name="dbkey" value="?" />
            </output>
        </test>
        <test>
            <!-- test cram output -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa" dbkey="hg19"/>
            <param name="fastq_input_selector" value="single"/>
            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
            <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
            <param name="analysis_type_selector" value="map-ont"/>
            <param name="output_format" value="CRAM"/>
            <output name="alignment_output" ftype="cram" file="winnowmap-test1-fasta.cram" lines_diff="2">
                <metadata name="dbkey" value="hg19" />
            </output>
        </test>
        <test>
            <!-- test paired input -->
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>

                    <element name="forward" value="bwa-mem-fastq1.fq" />
                    <element name="reverse" value="bwa-mem-fastq2.fq" />
                </collection>
            </param>
            <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
            <output name="alignment_output" ftype="bam" file="winnowmap-test2.bam" lines_diff="2"/>
        </test>
        <test>
            <!-- test data table reference -->
            <param name="reference_source_selector" value="cached" />
            <param name="ref_file" value="bwa-mem-mt-genome" dbkey="hg19"/>
            <param name="fastq_input_selector" value="single"/>
            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
            <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
            <param name="analysis_type_selector" value="map-ont"/>
            <section name="alignment_options">
                <param name="min_occ_floor" value="1000"/>
                <param name="A" value="2"/>
                <param name="B" value="8"/>
                <param name="O" value="12"/>
                <param name="O2" value="32"/>
                <param name="E" value="2"/>
                <param name="E2" value="1"/>
                <param name="z" value="400"/>
                <param name="s" value="40"/>
            </section>
            <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" >
                <metadata name="dbkey" value="bwa-mem-mt-genome-dbkey" />
            </output>
        </test>
        <test>
            <!-- test alignment options -->
            <param name="reference_source_selector" value="cached" />
            <param name="min_occ_floor" value="1000"/>

                <param name="E2" value="1" />
                <param name="z" value="400" />
                <param name="s" value="40" />
            </section>
            <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" />
            <assert_command>
                <has_text text="-A 2"/>
                <has_text text="-B 8"/>
                <has_text text="-O 12,32"/>
                <has_text text="-E 2,1"/>
                <has_text text="-z 400"/>
                <has_text text="-s 40"/>
            </assert_command>
        </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="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
            <param name="analysis_type_selector" value="map-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="winnowmap-self-homology.fasta" />