comparison hifiasm.xml @ 3:9ef6920c3089 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"

2:f3c89da3af16

<tool id="hifiasm" name="Hifiasm" version="@VERSION@+galaxy0">
    <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
    <macros>
        <token name="@VERSION@">0.15.3</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>

                --n-perturb $hic_partition.n_perturb
            #end if
            #if $hic_partition.f_perturb:
                --f-perturb $hic_partition.f_perturb
            #end if
        #end if

        ## Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option '--primary' to output primary assembly and alternate assembly.
        --primary
        $input_filenames

        ]]>
    </command>
    <inputs>
        <conditional name="mode">
            <param name="mode_selector" type="select" label="Assembly mode">

                <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" />
                <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" />
            </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" />
       
        <conditional name="advanced_options">
            <param name="advanced_selector" type="select" label="Advanced options">
                <option value="blank">Leave default</option>
                <option value="set">Specify</option>
            </param>

                <param argument="--h2" type="data" format="fastq,fastq.gz" multiple="true" label="Hi-C R2 reads" />
                <param argument="--seed" type="integer" min="1" value="" optional="true" label="RNG seed" />
                <param argument="--n-weight" type="integer" min="1" value="" optional="true" label="Rounds of reweighting Hi-C links" />
                <param argument="--n-perturb" type="integer" min="1" value="" optional="true" label="Rounds of perturbation" />
                <param argument="--f-perturb" type="float" min="0" max="1" value="" optional="true" label="Fraction to flip for perturbation" />
            </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>

            <filter>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>hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
            <param name="filter_bits" value="0" />

                <assert_contents>
                    <has_size value="0"/>
                </assert_contents>
            </output>
        </test>

        <!-- Test Hi-C
        <test>
            <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
            <param name="filter_bits" value="0" />
            <param name="mode_selector" value="standard" />
            <conditional name="hic_partition">
                <param name="hic_partition_selector" value="set"/>

3:9ef6920c3089

<tool id="hifiasm" name="Hifiasm" version="@VERSION@+galaxy0">
    <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
    <macros>
        <token name="@VERSION@">0.15.4</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>

                --n-perturb $hic_partition.n_perturb
            #end if
            #if $hic_partition.f_perturb:
                --f-perturb $hic_partition.f_perturb
            #end if
            --l-msjoin $hic_partition.l_msjoin
        #end if

        ## Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option '--primary' to output primary assembly and alternate assembly.
        --primary
        $input_filenames
        #if $log_out:
            2> output.log
        #end if
        ]]>
    </command>
    <inputs>
        <conditional name="mode">
            <param name="mode_selector" type="select" label="Assembly mode">

                <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" />
                <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" />
            </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" />
        <conditional name="advanced_options">
            <param name="advanced_selector" type="select" label="Advanced options">
                <option value="blank">Leave default</option>
                <option value="set">Specify</option>
            </param>

                <param argument="--h2" type="data" format="fastq,fastq.gz" multiple="true" label="Hi-C R2 reads" />
                <param argument="--seed" type="integer" min="1" value="" optional="true" label="RNG seed" />
                <param argument="--n-weight" type="integer" min="1" value="" optional="true" label="Rounds of reweighting Hi-C links" />
                <param argument="--n-perturb" type="integer" min="1" value="" optional="true" label="Rounds of perturbation" />
                <param argument="--f-perturb" type="float" min="0" max="1" value="" optional="true" label="Fraction to flip for perturbation" />
                <param argument="--l-msjoin" type="integer" min="0" value="500000" label="Detect misjoined unitigs of greater than or equal to specified size" help="A value of 0 disables this filter"/>
            </when> 
        </conditional>
        <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/> 
    </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>

            <filter>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} ${on_string}, HI-C hap2 balanced contig graph hap2">
            <filter>hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}, log file">
            <filter>log_out</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
            <param name="filter_bits" value="0" />

                <assert_contents>
                    <has_size value="0"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test logfile out-->
        <test>
            <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
            <param name="filter_bits" value="0" />
            <param name="mode_selector" value="standard" />
            <param name="log_out" value="yes"/>
            <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" ftype="gfa1">
                <assert_contents>
                    <has_size value="0"/>
                </assert_contents>
            </output>
            <output name="log_file" ftype="txt">
                <assert_contents>
                    <has_line line="[M::main] CMD: hifiasm -t 1 -o output -f 0 --primary input_0.fasta.gz"/>
                </assert_contents>
            </output>
        </test>

        <!-- Test Hi-C
        <test> 
            <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
            <param name="filter_bits" value="0" />
            <param name="mode_selector" value="standard" />
            <conditional name="hic_partition">
                <param name="hic_partition_selector" value="set"/>