comparison hifiasm.xml @ 8:5f625c63b8bc draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed

7:366a11d316a7

<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@">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>

        --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">

        </data>
        <!--Log output-->
        <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 expect_num_outputs="4">
            <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" />

                <assert_contents>
                    <has_size value="0"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <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" />

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test logfile out-->
        <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" />
            <param name="log_out" value="yes"/>
            <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />

                    <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 reads-->
        <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="hic_partition">
                <param name="hic_partition_selector" value="set"/>

                    <has_size value="59522" delta="500"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test trio mode -->
        <test expect_num_outputs="4">
            <param name="filter_bits" value="0"/>
            <conditional name="mode">
                <param name="mode_selector" value="trio"/>
                <param name="reads" value="child.fasta.gz"/>
                <param name="hap1_reads" value="paternal.fasta.gz"/>

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test ignore-error-corrected option -->
        <test expect_num_outputs="4">
            <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="assembly_selector" value="set"/>

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test expected haplotype number -->
        <test expect_num_outputs="4">
            <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">
                <param name="purge_selector" value="set"/>

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test min_hist_cnt option -->
        <test expect_num_outputs="4">
            <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">
                <param name="advanced_selector" value="set"/>

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test max_kooc option -->
        <test expect_num_outputs="4">
            <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">
                <param name="advanced_selector" value="set"/>

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test hg-size option -->
        <test expect_num_outputs="4">
            <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">
                <param name="advanced_selector" value="set"/>

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test ignore-error-corrected option -->
        <test expect_num_outputs="4">
            <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="assembly_selector" value="set"/>

8:5f625c63b8bc

<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@">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>

        --primary
        $input_filenames
        #if $log_out:
            2> output.log
        #end if
	    && mkdir noseq_files && mv *.noseq.gfa noseq_files
        ]]>
    </command>
    <inputs>
        <conditional name="mode">
            <param name="mode_selector" type="select" label="Assembly mode">

        </data>
        <!--Log output-->
        <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file">
            <filter>log_out</filter>
        </data>
        <collection name="noseq files" type="list" label="${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" />

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

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </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"/>
            <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />

                    <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 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">
                <param name="hic_partition_selector" value="set"/>

                    <has_size value="59522" 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"/>
                <param name="hap1_reads" value="paternal.fasta.gz"/>

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </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="assembly_selector" value="set"/>

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </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">
                <param name="purge_selector" value="set"/>

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </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">
                <param name="advanced_selector" value="set"/>

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </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">
                <param name="advanced_selector" value="set"/>

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </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">
                <param name="advanced_selector" value="set"/>

                    <has_size value="0"/>
                </assert_contents>
            </output>
        </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="assembly_selector" value="set"/>