comparison hifiasm_meta.xml @ 2:fa35f1106d3e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta commit bc8759245f44924d0122276e42f02fc1f1190e50

1:15dbb444df71

        #################
        ## RUN HIFIASM ##
        #################

        hifiasm_meta 
        --lowq-10 '$read_selection.lowq_10'
        --lowq-3 '$read_selection.lowq_3'
        --lowq-5 '$read_selection.lowq_5'
        -a '$assembly.a'
        #if $f:
            -f '$f'
        #end if
        -k '$overlap_correction.k'
        -o asm
        -r '$overlap_correction.r'
        $read_selection.S
        -t \${GALAXY_SLOTS:-4}
        '$reads_fn'

    ]]></command>
    <inputs>
        <param name="reads" format="fastqsanger,fastqsanger.gz" type="data" label="HiFi reads" help="Input reads for assembly" />
        <!-- This hidden parameter is only used to save RAM for planemo test. -->
        <!-- See https://github.com/galaxyproject/tools-iuc/pull/5033#issuecomment-1382915060 -->
        <param type="hidden" optional="true" argument="-f" />
        <section name="read_selection" title="Read selection" expanded="false">
            <param argument='-S' type="boolean" checked="true" truevalue="-S" falsevalue="" label="Enable read selection" help="If enabled, hifiasm_meta will estimate the total number of read overlaps." />
            <param argument='--lowq-10' type="integer" value='50' label="lower 10% runtime kmer frequency threshold." />
            <param argument='--lowq-5' type="integer" value='50' label="lower 5% runtime kmer frequency threshold." />
            <param argument='--lowq-3' type="integer" value='10' label="lower 3% runtime kmer frequency threshold." />
        </section>
        <section name="overlap_correction" title="Overlap/Error correction" expanded="false">
            <param argument='-k' type="integer" value='51' min="1" max="63" label="k-mer length" />
            <param argument='-r' type="integer" value='3' min="1" max="10" label="rounds of correction" />
        </section>

            <output_collection name="contig_graphs" type="list">
                <element name="Primary contigs" file="asm.p_ctg.gfa"/>
                <element name="Alternate contigs" file="asm.a_ctg.gfa"/>
            </output_collection>
        </test>
    </tests>
        <help><![CDATA[
hifiasm_meta
------------

2:fa35f1106d3e

        #################
        ## RUN HIFIASM ##
        #################

        hifiasm_meta 

        ## bloom filter parameter
        #if $f:
            -f '$f'
        #end if

        ## read selection parameters
        #if $read_selection.forced_read_selection.force_rs == "yes":
            --force-rs
            --lowq-10 '$read_selection.forced_read_selection.lowq_10'
            --lowq-3 '$read_selection.forced_read_selection.lowq_3'
            --lowq-5 '$read_selection.forced_read_selection.lowq_5'
        #else
            $read_selection.forced_read_selection.S
        #end if
    
        -a '$assembly.a'
        -k '$overlap_correction.k'
        -o asm
        -r '$overlap_correction.r'
        -t \${GALAXY_SLOTS:-4}
        '$reads_fn'

    ]]></command>
    <inputs>
        <param name="reads" format="fastqsanger,fastqsanger.gz" type="data" label="HiFi reads" help="Input reads for assembly" />
        <!-- This hidden parameter is only used to save RAM for planemo test. -->
        <!-- See https://github.com/galaxyproject/tools-iuc/pull/5033#issuecomment-1382915060 -->
        <param type="hidden" optional="true" argument="-f" />
        <section name="read_selection" title="Read selection" expanded="false">
            <conditional name="forced_read_selection">
                <param argument="--force-rs" type="select" label="Force read selection" help="Drop reads according to configurable runtime kmer frequency thresholds">
                    <option value="no" selected="true">No</option>
                    <option value="yes">Yes</option>                    
                </param>
                <when value="yes">
                    <param argument='--lowq-10' type="integer" value='50' label="Lower 10% runtime kmer frequency threshold" />
                    <param argument='--lowq-5' type="integer" value='50' label="Lower 5% runtime kmer frequency threshold" />
                    <param argument='--lowq-3' type="integer" value='10' label="Lower 3% runtime kmer frequency threshold" />
                </when>
                <when value="no">
                    <param argument='-S' type="boolean" checked="false" truevalue="-S" falsevalue="" label="Enable read selection" help="If enabled, hifiasm_meta will estimate the total number of read overlaps. If the estimation seems acceptable, no read will be dropped; otherwise, reads will be dropped from the most redundant ones until the criteria are satisfied. This can only be enabled if forced read selection is disabled." />
                </when>
            </conditional>
        </section>
        <section name="overlap_correction" title="Overlap/Error correction" expanded="false">
            <param argument='-k' type="integer" value='51' min="1" max="63" label="k-mer length" />
            <param argument='-r' type="integer" value='3' min="1" max="10" label="rounds of correction" />
        </section>

            <output_collection name="contig_graphs" type="list">
                <element name="Primary contigs" file="asm.p_ctg.gfa"/>
                <element name="Alternate contigs" file="asm.a_ctg.gfa"/>
            </output_collection>
        </test>
        <!-- 02: forced read selection -->
        <test>
            <param name="reads" value="tiny.fa.gz" />
            <param name='f' value="0" />
            <param name='force_rs' value='yes' />
            <output_collection name="contig_graphs" type="list">
                <element name="Primary contigs">
                    <assert_contents>
                        <has_size value="93053" delta="30000" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <!-- 03: read selection -->
        <test>
            <param name="reads" value="zymoD6331std-ecoli-ten-percent.42.1.fq.gz" />
            <param name='f' value="0" />
            <param name='force_rs' value='no' />
            <param name='S' value='true' />
            <output_collection name="contig_graphs" type="list">
                <element name="Primary contigs" file="S.p_ctg.gfa"/>
                <element name="Alternate contigs" file="S.a_ctg.gfa"/>
            </output_collection>
        </test>
    </tests>
        <help><![CDATA[
hifiasm_meta
------------