comparison hifiasm.xml @ 7:366a11d316a7 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4

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>

            <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 ${on_string}: raw initig graph">
            <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed initig graph">

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

                <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">
            <param name="filter_bits" value="0"/>
            <conditional name="mode">

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>

            <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} ${on_string}: Hi-C hap2 balanced contig graph hap2">
            <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <data name="hic_raw_initig" format="gfa1" from_work_dir="output.hic.r_utg.gfa" label="${tool.name} ${on_string}: Hi-C raw unitig">
            <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <!--Trio outputs with Hi-c reads-->
        <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph">
            <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
        </data>
        <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed initig graph">

                    <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"/>

                <assert_contents>
                    <has_text_matching expression="^S" />
                    <has_size value="59529" delta="500"/>
                </assert_contents>
            </output>
            <output name="hic_raw_initig" ftype="gfa1" >
                <assert_contents>
                    <has_text_matching expression="^S" />
                    <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">