comparison hifiasm.xml @ 6:5bec28269d95 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75"

5:045c7c3d8e59

<tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
    <macros>
        <token name="@TOOL_VERSION@">0.16.1</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
        <xml name="reads">
            <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
        </xml>
    </macros>

                <param name="drop_kmers" argument="-D" type="float" value="5.0" label="Drop k-mers" help="K-mers that occur more than this value multiplied by the coverage will be discarded" />
                <param name="max_overlaps" argument="-N" type="integer" value="100" label="Maximum overlaps to consider" help="The software selects the larger of this value and the k-mer count multiplied by coverage" />
                <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds" />
                <param argument="--min-hist-cnt" type="integer" min="0" value="" optional="true" label="Minimum count threshold" help="When analyzing the k-mer spectrum, ignore counts below this value" />
                <param argument="--max-kocc" type="integer" min="0" value="20000" label="Maximum k-mer ocurrence" help="Employ k-mers occurring less than INT times to rescue repetitive overlaps" />
                <param argument="--hg-size" type="text" value="" optional="true" label="Estimated haploid genome size" help="Estimated haploid genome size used for inferring read coverage. If not provided, this parameter will be infered by hifism. Common suffices are required, for example, 100m or 3g">
                    <sanitizer invalid_char="">
                        <valid initial="string.digits">
                            <add value="k" />
                            <add value="K" />
                            <add value="m" />

            <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <data name="hic_acontig_graph" format="gfa1" from_work_dir="output.hic.a_ctg.gfa" label="${tool.name} ${on_string}: Hi-C alternate contig graph">
            <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.bp.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1">
            <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.bp.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2">
            <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <!--Trio outputs with Hi-c reads-->
        <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph">
            <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>

            </conditional>
            <output name="hic_pcontig_graph" file="hifiasm-out-hifi-p.gfa" ftype="gfa1" />
            <output name="hic_acontig_graph" file="hifiasm-out-hifi-a.gfa" ftype="gfa1" />
            <output name="hic_balanced_contig_hap1_graph" ftype="gfa1">
                <assert_contents>
                    <has_size value="0"/>
                </assert_contents>
            </output>
            <output name="hic_balanced_contig_hap1_graph" ftype="gfa1" >
                <assert_contents>
                    <has_size value="0"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test trio mode -->
        <test expect_num_outputs="4">

6:5bec28269d95

<tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
    <macros>
        <token name="@TOOL_VERSION@">0.16.1</token>
        <token name="@VERSION_SUFFIX@">2</token>
        <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
        <xml name="reads">
            <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
        </xml>
    </macros>

                <param name="drop_kmers" argument="-D" type="float" value="5.0" label="Drop k-mers" help="K-mers that occur more than this value multiplied by the coverage will be discarded" />
                <param name="max_overlaps" argument="-N" type="integer" value="100" label="Maximum overlaps to consider" help="The software selects the larger of this value and the k-mer count multiplied by coverage" />
                <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds" />
                <param argument="--min-hist-cnt" type="integer" min="0" value="" optional="true" label="Minimum count threshold" help="When analyzing the k-mer spectrum, ignore counts below this value" />
                <param argument="--max-kocc" type="integer" min="0" value="20000" label="Maximum k-mer ocurrence" help="Employ k-mers occurring less than INT times to rescue repetitive overlaps" />
                <param argument="--hg-size" type="text" value="" optional="true" label="Estimated haploid genome size"
                       help="Estimated haploid genome size used for inferring read coverage. If not provided, this parameter will be infered by hifism. Common suffices are required, for example, 100m or 3g">
                    <sanitizer invalid_char="">
                        <valid initial="string.digits">
                            <add value="k" />
                            <add value="K" />
                            <add value="m" />

            <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <data name="hic_acontig_graph" format="gfa1" from_work_dir="output.hic.a_ctg.gfa" label="${tool.name} ${on_string}: Hi-C alternate contig graph">
            <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.hic.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1">
            <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2">
            <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <!--Trio outputs with Hi-c reads-->
        <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph">
            <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>

            </conditional>
            <output name="hic_pcontig_graph" file="hifiasm-out-hifi-p.gfa" ftype="gfa1" />
            <output name="hic_acontig_graph" file="hifiasm-out-hifi-a.gfa" ftype="gfa1" />
            <output name="hic_balanced_contig_hap1_graph" ftype="gfa1">
                <assert_contents>
                    <has_text_matching expression="^S" />
                    <has_size value="59529" delta="500"/>
                </assert_contents>
            </output>
            <output name="hic_balanced_contig_hap1_graph" ftype="gfa1" >
                <assert_contents>
                    <has_text_matching expression="^S" />
                    <has_size value="59529" delta="500"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test trio mode -->
        <test expect_num_outputs="4">