comparison hifiasm.xml @ 10:2061fb3b81b4 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa

9:c388a21dcbf1

<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@">0.18.5</token>
        <token name="@VERSION_SUFFIX@">0</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>

        #set $input_files = list()
        #set $hap1_inputs = list()
        #set $hap2_inputs = list()
        #set $hic1_inputs = list()
        #set $hic2_inputs = list()
        #for idx, read in enumerate($mode.reads):
            #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension)
            ln -s '$read' $inputfile &&
            $input_files.append($inputfile)
        #end for

                #set $inputfile = './HiCR/input_%d.%s' % ($idx, $read.dataset.extension)
                ln -s '$read' $inputfile &&
                $hic2_inputs.append($inputfile)
            #end for
        #end if
        #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)

                --n-hap $purge_options.n_hap
            #end if
        #end if

        #if str($hic_partition.hic_partition_selector) == 'set':
            --h1 '${ ' '.join(["%s" % $x for $x in $hic1_inputs]) }'
            --h2 '${ ' '.join(["%s" % $x for $x in $hic2_inputs]) }'
            #if $hic_partition.seed:
                --seed $hic_partition.seed
            #end if
            #if $hic_partition.n_weight:
                --n-weight $hic_partition.n_weight

            #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

                <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. Increasing this may improves phasing results but takes longer time" />
                <param argument="--n-perturb" type="integer" min="1" value="" optional="true" label="Rounds of perturbation. Increasing this may improves phasing results but takes longer time" />
                <param argument="--f-perturb" type="float" min="0" max="1" value="" optional="true" label="Fraction to flip for perturbation. Increasing this may improves phasing results but takes longer time" />
                <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>
        <conditional name="advanced_options">
            <param name="advanced_selector" type="select" label="Advanced options">
                <option value="blank">Leave default</option>

        <collection name="noseq_files" type="list" label="${tool.name} on ${on_string}: noseq files">
            <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="noseq_files" />
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="5">
            <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
            <param name="filter_bits" value="0" />
            <param name="mode_selector" value="standard" />
            <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" />
        </test>
        <test expect_num_outputs="5">
            <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" />
        </test>
        <!-- Test logfile out-->
        <test expect_num_outputs="6">
            <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"/>

                <assert_contents>
                    <has_text text="-o output -f 0 --primary input_0.fasta.gz"/>
                </assert_contents>
            </output>
        </test>
        <!--Test Hi-C reads-->
        <test expect_num_outputs="6"> 
            <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">

                    <has_text_matching expression="^S" />
                    <has_size value="83904" delta="500"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test trio mode -->
        <test expect_num_outputs="5">
            <param name="filter_bits" value="0"/>
            <conditional name="mode">
                <param name="mode_selector" value="trio"/>
                <param name="reads" value="child.fasta.gz"/>

                <has_text text="-1 hap1.yak" />
                <has_text text="-2 hap2.yak" />
                <has_text text="--primary" />
            </assert_command>
        </test>
        <!-- Test ignore-error-corrected option -->
        <test expect_num_outputs="5">
            <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="assembly_options">

            </conditional>
            <output name="raw_unitigs" file="hifiasm-out3-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out3-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out3-primary.gfa" ftype="gfa1" />
        </test>
        <!-- Test expected haplotype number -->
        <test expect_num_outputs="5">
            <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="purge_options">

            </conditional>
            <output name="raw_unitigs" file="hifiasm-out4-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out4-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out4-primary.gfa" ftype="gfa1" />
        </test>
        <!-- Test min_hist_cnt option -->
        <test expect_num_outputs="5">
            <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="advanced_options">

            </conditional>
            <output name="raw_unitigs" file="hifiasm-out5-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out5-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out5-primary.gfa" ftype="gfa1" />
        </test>
        <!-- Test max_kooc option -->
        <test expect_num_outputs="5">
            <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="advanced_options">

            </conditional>
            <output name="raw_unitigs" file="hifiasm-out6-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out6-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out6-primary.gfa" ftype="gfa1" />
        </test>
        <!-- Test hg-size option -->
        <test expect_num_outputs="5">
            <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="advanced_options">

            </conditional>
            <output name="raw_unitigs" file="hifiasm-out7-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out7-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out7-primary.gfa" ftype="gfa1" />
        </test>
        <!-- Test ignore-error-corrected option -->
        <test expect_num_outputs="5">
            <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="assembly_options">

                <param name="hom-cov" value="1000"/>
            </conditional>
            <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

10:2061fb3b81b4

<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@">0.18.5</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>

        #set $input_files = list()
        #set $hap1_inputs = list()
        #set $hap2_inputs = list()
        #set $hic1_inputs = list()
        #set $hic2_inputs = list()
        #set $ultralong_inputs = list()
        #for idx, read in enumerate($mode.reads):
            #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension)
            ln -s '$read' $inputfile &&
            $input_files.append($inputfile)
        #end for

                #set $inputfile = './HiCR/input_%d.%s' % ($idx, $read.dataset.extension)
                ln -s '$read' $inputfile &&
                $hic2_inputs.append($inputfile)
            #end for
        #end if
        #if str($ont_integration.ont_integration_selector) == 'set'
            mkdir ultralong &&
            #for idx, read in enumerate($ont_integration.ul):
                #set $inputfile = './ultralong/input_%d.%s' % ($idx, $read.dataset.extension)
                ln -s '$read' $inputfile &&
                $ultralong_inputs.append($inputfile)
            #end for
        #end if
        #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)

                --n-hap $purge_options.n_hap
            #end if
        #end if

        #if str($hic_partition.hic_partition_selector) == 'set':
            --h1 ${ ' '.join(["'%s'" % $x for $x in $hic1_inputs]) }
            --h2 ${ ' '.join(["'%s'" % $x for $x in $hic2_inputs]) }
            #if $hic_partition.seed:
                --seed $hic_partition.seed
            #end if
            #if $hic_partition.n_weight:
                --n-weight $hic_partition.n_weight

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

        #if str($ont_integration.ont_integration_selector) == 'set':
            --ul ${ ' '.join(["'%s'" % $x for $x in $ultralong_inputs]) }
            #if $ont_integration.ul_rate:
                --ul-rate $ont_integration.ul_rate
            #end if
            #if $ont_integration.ul_tip:
                --ul-tip $ont_integration.ul_tip
            #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

                <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. Increasing this may improves phasing results but takes longer time" />
                <param argument="--n-perturb" type="integer" min="1" value="" optional="true" label="Rounds of perturbation. Increasing this may improves phasing results but takes longer time" />
                <param argument="--f-perturb" type="float" min="0" max="1" value="" optional="true" label="Fraction to flip for perturbation. Increasing this may improves phasing results but takes longer time" />
                <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>
        <conditional name="ont_integration">
            <param name="ont_integration_selector" type="select" label="Options for ONT integration">
                <option value="blank">Leave default</option>
                <option value="set">Specify</option>
            </param>
            <when value="blank" />
            <when value="set">
                <param argument="--ul" type="data" format="fastq,fastq.gz,fasta,fasta.gz" multiple="true" label="Ultra-long (>10kb) reads" />
                <param argument="--ul-rate" type="float" value="0.2" optional="true" label="error rate of ultra-long reads (default 0.2)" />
                <param argument="--ul-tip" type="integer" value="6" optional="true" label="remove tip unitigs composed of less than (INT) reads for the UL assembly (default 6)" />
            </when>
        </conditional>
        <conditional name="advanced_options">
            <param name="advanced_selector" type="select" label="Advanced options">
                <option value="blank">Leave default</option>

        <collection name="noseq_files" type="list" label="${tool.name} on ${on_string}: noseq files">
            <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="noseq_files" />
        </collection>
    </outputs>
    <tests>
        <!-- TEST 1 -->
        <test expect_num_outputs="5">
            <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
            <param name="filter_bits" value="0" />
            <param name="mode_selector" value="standard" />
            <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" />
        </test>
        <!-- TEST 2 -->
        <test expect_num_outputs="5">
            <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" />
        </test>
        <!-- TEST 3: Test logfile out-->
        <test expect_num_outputs="6">
            <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"/>

                <assert_contents>
                    <has_text text="-o output -f 0 --primary input_0.fasta.gz"/>
                </assert_contents>
            </output>
        </test>
        <!--TEST 4: Test Hi-C reads-->
        <test expect_num_outputs="6"> 
            <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">

                    <has_text_matching expression="^S" />
                    <has_size value="83904" delta="500"/>
                </assert_contents>
            </output>
        </test>
        <!-- TEST 5: Test trio mode -->
        <test expect_num_outputs="5">
            <param name="filter_bits" value="0"/>
            <conditional name="mode">
                <param name="mode_selector" value="trio"/>
                <param name="reads" value="child.fasta.gz"/>

                <has_text text="-1 hap1.yak" />
                <has_text text="-2 hap2.yak" />
                <has_text text="--primary" />
            </assert_command>
        </test>
        <!-- TEST 6: Test ignore-error-corrected option -->
        <test expect_num_outputs="5">
            <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="assembly_options">

            </conditional>
            <output name="raw_unitigs" file="hifiasm-out3-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out3-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out3-primary.gfa" ftype="gfa1" />
        </test>
        <!-- TEST 7: Test expected haplotype number -->
        <test expect_num_outputs="5">
            <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="purge_options">

            </conditional>
            <output name="raw_unitigs" file="hifiasm-out4-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out4-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out4-primary.gfa" ftype="gfa1" />
        </test>
        <!-- TEST 8: Test min_hist_cnt option -->
        <test expect_num_outputs="5">
            <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="advanced_options">

            </conditional>
            <output name="raw_unitigs" file="hifiasm-out5-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out5-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out5-primary.gfa" ftype="gfa1" />
        </test>
        <!-- TEST 9: Test max_kooc option -->
        <test expect_num_outputs="5">
            <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="advanced_options">

            </conditional>
            <output name="raw_unitigs" file="hifiasm-out6-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out6-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out6-primary.gfa" ftype="gfa1" />
        </test>
        <!-- TEST 10: Test hg-size option -->
        <test expect_num_outputs="5">
            <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="advanced_options">

            </conditional>
            <output name="raw_unitigs" file="hifiasm-out7-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out7-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out7-primary.gfa" ftype="gfa1" />
        </test>
        <!-- TEST 11: Test ignore-error-corrected option -->
        <test expect_num_outputs="5">
            <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="assembly_options">

                <param name="hom-cov" value="1000"/>
            </conditional>
            <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1" />
            <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1" />
            <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1" />
        </test>
        <!-- TEST 12: test nanopore input -->
        <test expect_num_outputs="5">
            <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
            <param name="mode_selector" value="standard" />
	        <param name="filter_bits" value="0" />
            <conditional name="ont_integration">
                <param name="ont_integration_selector" value="set" />
                <param name="ul" value="nanopore.first5.fasta.gz" />
                <param name="ul_tip" value="1" />
            </conditional>
            <output name="primary_contig_graph" file="hifiasm-out-hifiul.bp.p_ctg.gfa" ftype="gfa1" />
            <output name="raw_unitigs" file="hifiasm-out-hifiul.bp.r_utg.gfa" ftype="gfa1" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark