comparison hifiasm.xml @ 1:6505bd37670d draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"

0:bf0a4667e3ce

<tool id="hifiasm" name="Hifiasm" version="@VERSION@">
    <description>de novo assembler</description>
    <macros>
        <token name="@VERSION@">0.14</token>
        <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
        <xml name="reads">
            <param name="reads" type="data" format="@FORMATS@" label="Input reads" />
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">hifiasm</requirement>
        <requirement type="package" version="0.1">yak</requirement>
    </requirements>
    <version_command>hifiasm --version</version_command>
    <command detect_errors="exit_code">
        <![CDATA[
        #if str($mode.mode_selector) == 'standard':
            ln -s '$mode.reads' input.${mode.reads.extension} &&
        #else:
            ln -s '$mode.hap1_reads' hap1_reads.${mode.hap1_reads.extension} &&
            ln -s '$mode.hap2_reads' hap2_reads.${mode.hap2_reads.extension} &&
            yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap1.yak hap1_reads.${mode.hap1_reads.extension} &&
            yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap2.yak hap2_reads.${mode.hap2_reads.extension} &&
        #end if
        hifiasm -i input.${mode.reads.extension} -t \${GALAXY_SLOTS:-1} -o output -f $filter_bits
        #if str($advanced_options.advanced_selector) == 'set':
            -z $advanced_options.adapter_length
            -k $advanced_options.kmer_length
            -w $advanced_options.window_size
            -D $advanced_options.drop_kmers

            -p $assembly_options.pop_unitigs
            -n $assembly_options.remove_tips
            -x $assembly_options.max_overlap
            -y $assembly_options.min_overlap
            $assembly_options.disable_post_join
            --pb-range $assembly_options.pb_range
        #end if
        #if str($mode.mode_selector) == 'trio':
            -1 hap1.yak
            -2 hap2.yak
            -c $mode.max_kmers

            <when value="standard">
                <expand macro="reads" />
            </when>
            <when value="trio">
                <expand macro="reads" />
                <param name="hap1_reads" type="data" format="fastq,fastq.gz" label="Haplotype 1 reads" />
                <param name="hap2_reads" type="data" format="fastq,fastq.gz" label="Haplotype 2 reads" />
                <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer's frequency" />
                <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" />
            </when>
        </conditional>
        <param name="filter_bits" argument="-f" type="integer" min="0" value="37" label="Bits for bloom filter" help="A value of 0 disables the bloom filter" />

                <param name="pop_unitigs" argument="-p" type="integer" value="100000" label="Minimum unitig bubble size" help="Pop unitig graph bubbles smaller than this value" />
                <param name="remove_tips" argument="-n" type="integer" value="3" label="Tip unitigs" help="Keep only tip unitigs with a number of reads greater than or equal to this value" />
                <param name="max_overlap" argument="-x" type="float" min="0" max="1" value="0.8" label="Maximum overlap drop ratio" />
                <param name="min_overlap" argument="-y" type="float" min="0" max="1" value="0.2" label="Minimum overlap drop ratio" />
                <param name="disable_post_join" argument="-u" type="boolean" truevalue="-u" falsevalue="" label="Skip post join contigs step" help="May improve N50" />
                <param argument="--pb-range" type="integer" min="0" max="100" value="0" label="Inconsistent contigs" help="If this option is set to a value greater than zero the tool generates an additional BED dataset containing regions that are &gt;= x% inconsistent." />
            </when>
        </conditional>
        <conditional name="purge_options">
            <param name="purge_selector" type="select" label="Options for purging duplicates">
                <option value="blank">Leave default</option>

                <param argument="--high-het" type="boolean" truevalue="--high-het" falsevalue="" label="Experimental high-heterozygosity mode" help="NB: May be unstable" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string} Haplotype-resolved raw unitig graph">
            <filter>mode['mode_selector'] == 'standard'</filter>
        </data>
        <data name="raw_unitigs" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string} Haplotype-resolved raw unitig graph">
            <filter>mode['mode_selector'] == 'trio'</filter>
        </data>
        <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string} Processed unitig graph">
            <filter>mode['mode_selector'] == 'standard'</filter>
        </data>
        <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string} Primary assembly contig graph">
            <filter>mode['mode_selector'] == 'standard'</filter>
        </data>
        <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string} Alternate assembly contig graph">
            <filter>mode['mode_selector'] == 'standard'</filter>
        </data>
        <data name="hap1_contigs" format="gfa1" from_work_dir="output.hap1.p_ctg.gfa" label="${tool.name} ${mode.hap1_reads.name} contig graph">
            <filter>mode['mode_selector'] == 'trio'</filter>
        </data>
        <data name="hap2_contigs" format="gfa1" from_work_dir="output.hap2.p_ctg.gfa" label="${tool.name} ${mode.hap2_reads.name} contig graph">
            <filter>mode['mode_selector'] == 'trio'</filter>
        </data>
    </outputs>
    <tests>
        <test>

            <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
            <output name="alternate_contig_graph" file="hifiasm-out1-alternate.gfa" ftype="gfa1" />
        </test>
    </tests>
    <help><![CDATA[
***********************************
HiFiASM - a fast de novo assembler
***********************************

- *Minimum unitig bubble* size Pop unitig graph bubbles smaller than this value
- *Tip unitigs* Keep only tip unitigs with a number of reads greater than or equal to this value
- *Maximum overlap drop ratio*
- *Minimum overlap drop ratio*
- *Skip post join contigs step*  disable post join contigs step which may improve N50
- *Inconsistent contigs* If this option is set to a value greater than zero the tool generates an additional BED dataset containing regions that are >= x% inconsistent.

#### Options for purging duplicates
- *Purge level* 0: no purging; 1: light; 2: aggressive [0 for trio; 2 for unzip]
- *Similarity threshold for duplicate haplotigs*
- *Minimum overlapped reads for duplicate haplotigs*

1:6505bd37670d

<tool id="hifiasm" name="Hifiasm" version="@VERSION@+galaxy0">
    <description>de novo assembler</description>
    <macros>
        <token name="@VERSION@">0.14</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>
    <requirements>
        <requirement type="package" version="@VERSION@">hifiasm</requirement>
        <requirement type="package" version="0.1">yak</requirement>
    </requirements>
    <version_command>hifiasm --version</version_command>
    <command detect_errors="exit_code">
        <![CDATA[
        #set $input_files = list()
        #set $hap1_inputs = list()
        #set $hap2_inputs = list()
        #for idx, read in enumerate($mode.reads):
            #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension)
            ln -s '$read' $inputfile &&
            $input_files.append($inputfile)
        #end for
        #set $input_filenames = ' '.join($input_files)
        #if str($mode.mode_selector) == 'trio':
            #for idx, read in enumerate($mode.hap1_reads):
                #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension)
                ln -s '$read' $inputfile &&
                $hap1_inputs.append($inputfile)
            #end for
            #for idx, read in enumerate($mode.hap2_reads):
                #set $inputfile = 'hap2_input_%d.%s' % ($idx, $read.dataset.extension)
                ln -s '$read' $inputfile &&
                $hap2_inputs.append($inputfile)
            #end for
            #set $hap1_filenames = ' '.join($hap1_inputs)
            #set $hap2_filenames = ' '.join($hap2_inputs)
            yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames &&
            yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames &&
        #end if
        hifiasm -i $input_filenames -t \${GALAXY_SLOTS:-1} -o output -f $filter_bits
        #if str($mode.mode_selector) == 'trio':
            -1 hap1.yak -2 hap2.yak
        #end if
        #if str($advanced_options.advanced_selector) == 'set':
            -z $advanced_options.adapter_length
            -k $advanced_options.kmer_length
            -w $advanced_options.window_size
            -D $advanced_options.drop_kmers

            -p $assembly_options.pop_unitigs
            -n $assembly_options.remove_tips
            -x $assembly_options.max_overlap
            -y $assembly_options.min_overlap
            $assembly_options.disable_post_join
        #end if
        #if str($mode.mode_selector) == 'trio':
            -1 hap1.yak
            -2 hap2.yak
            -c $mode.max_kmers

            <when value="standard">
                <expand macro="reads" />
            </when>
            <when value="trio">
                <expand macro="reads" />
                <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads" />
                <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads" />
                <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer's frequency" />
                <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" />
            </when>
        </conditional>
        <param name="filter_bits" argument="-f" type="integer" min="0" value="37" label="Bits for bloom filter" help="A value of 0 disables the bloom filter" />

                <param name="pop_unitigs" argument="-p" type="integer" value="100000" label="Minimum unitig bubble size" help="Pop unitig graph bubbles smaller than this value" />
                <param name="remove_tips" argument="-n" type="integer" value="3" label="Tip unitigs" help="Keep only tip unitigs with a number of reads greater than or equal to this value" />
                <param name="max_overlap" argument="-x" type="float" min="0" max="1" value="0.8" label="Maximum overlap drop ratio" />
                <param name="min_overlap" argument="-y" type="float" min="0" max="1" value="0.2" label="Minimum overlap drop ratio" />
                <param name="disable_post_join" argument="-u" type="boolean" truevalue="-u" falsevalue="" label="Skip post join contigs step" help="May improve N50" />
            </when>
        </conditional>
        <conditional name="purge_options">
            <param name="purge_selector" type="select" label="Options for purging duplicates">
                <option value="blank">Leave default</option>

                <param argument="--high-het" type="boolean" truevalue="--high-het" falsevalue="" label="Experimental high-heterozygosity mode" help="NB: May be unstable" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph">
            <filter>mode['mode_selector'] == 'standard'</filter>
        </data>
        <data name="raw_unitigs" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph">
            <filter>mode['mode_selector'] == 'trio'</filter>
        </data>
        <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}, processed unitig graph">
            <filter>mode['mode_selector'] == 'standard'</filter>
        </data>
        <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}, primary assembly contig graph">
            <filter>mode['mode_selector'] == 'standard'</filter>
        </data>
        <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}, alternate assembly contig graph">
            <filter>mode['mode_selector'] == 'standard'</filter>
        </data>
        <data name="hap1_contigs" format="gfa1" from_work_dir="output.hap1.p_ctg.gfa" label="${tool.name} ${mode.hap1_reads.name}, contig graph">
            <filter>mode['mode_selector'] == 'trio'</filter>
        </data>
        <data name="hap2_contigs" format="gfa1" from_work_dir="output.hap2.p_ctg.gfa" label="${tool.name} ${mode.hap2_reads.name}, contig graph">
            <filter>mode['mode_selector'] == 'trio'</filter>
        </data>
    </outputs>
    <tests>
        <test>

            <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
            <output name="alternate_contig_graph" file="hifiasm-out1-alternate.gfa" ftype="gfa1" />
        </test>
        <test>
            <param name="reads" value="hifiasm-in2-0.fa.gz,hifiasm-in2-1.fa.gz,hifiasm-in2-2.fa.gz,hifiasm-in2-3.fa.gz,hifiasm-in2-4.fa.gz" ftype="fasta.gz" />
            <param name="filter_bits" value="0" />
            <param name="mode_selector" value="standard" />
            <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out2-primary.gfa" ftype="gfa1" />
            <output name="alternate_contig_graph" file="hifiasm-out2-alternate.gfa" ftype="gfa1" />
        </test>
    </tests>
    <help><![CDATA[
***********************************
HiFiASM - a fast de novo assembler
***********************************

- *Minimum unitig bubble* size Pop unitig graph bubbles smaller than this value
- *Tip unitigs* Keep only tip unitigs with a number of reads greater than or equal to this value
- *Maximum overlap drop ratio*
- *Minimum overlap drop ratio*
- *Skip post join contigs step*  disable post join contigs step which may improve N50

#### Options for purging duplicates
- *Purge level* 0: no purging; 1: light; 2: aggressive [0 for trio; 2 for unzip]
- *Similarity threshold for duplicate haplotigs*
- *Minimum overlapped reads for duplicate haplotigs*