comparison abyss-pe.xml @ 12:a929ce596a34 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit c083399ddb31b026aaab1d600d8789bf56cf4d4b

11:7547fcab5d19

<tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>de novo sequence assembler</description>
    <macros>
        <token name="@TOOL_VERSION@">2.3.6</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <xml name="reads_conditional">
            <conditional name="reads">
                <param name="reads_selector" type="select" label="Type of paired-end datasets">
                    <option value="paired">2 separate datasets</option>
                    <option value="paired_collection">1 paired dataset collection</option>

#end if

abyss-pe
name=abyss
j=\${GALAXY_SLOTS:-1}
B=\${GALAXY_MEMORY_MB:-2048}M
k=$k

#if str($K)
    K=$K
#end if

        <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />
        <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" />
    </outputs>

    <tests>
        <test>
            <repeat name="lib_repeat">
                <conditional name="reads">
                    <param name="reads_selector" value="paired" />
                    <param name="reads1" ftype="fastqsanger.gz" value="assembly_sample-R1.fastq.gz" />
                    <param name="reads2" ftype="fastqsanger.gz" value="assembly_sample-R2.fastq.gz" />

            <output name="contigs_outfile" file="abyss-contigs1.fa" />
            <output name="scaffolds" file="abyss-scaffolds1.fa" />
            <output name="indels" file="empty_file.fasta" />
            <output name="stats" file="abyss-stats1.tab" />
        </test>
        <test>
            <param name="se_reads" ftype="fastq.gz" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
            <param name="k" value="50" />
            <output name="unitigs" file="abyss-unitigs2.fa" />
            <output name="indels" file="empty_file.fasta" />
            <output name="stats" file="abyss-stats2.tab" />
        </test>
        <test>
            <param name="se_reads" ftype="fasta" value="assembly_sample-R1.fasta,assembly_sample-R2.fasta" />
            <param name="long_seqs" ftype="fasta" value="assembly_sample-R2.fasta" />
            <param name="k" value="50" />
            <output name="unitigs" file="abyss-unitigs3.fa" />
            <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />

12:a929ce596a34

<tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>de novo sequence assembler</description>
    <macros>
        <token name="@TOOL_VERSION@">2.3.6</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <xml name="reads_conditional">
            <conditional name="reads">
                <param name="reads_selector" type="select" label="Type of paired-end datasets">
                    <option value="paired">2 separate datasets</option>
                    <option value="paired_collection">1 paired dataset collection</option>

#end if

abyss-pe
name=abyss
j=\${GALAXY_SLOTS:-1}
B=\$((\${GALAXY_MEMORY_MB:-2048} * 9 /10 ))M

k=$k

#if str($K)
    K=$K
#end if

        <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />
        <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" />
    </outputs>

    <tests>
        <test expect_num_outputs="5">
            <repeat name="lib_repeat">
                <conditional name="reads">
                    <param name="reads_selector" value="paired" />
                    <param name="reads1" ftype="fastqsanger.gz" value="assembly_sample-R1.fastq.gz" />
                    <param name="reads2" ftype="fastqsanger.gz" value="assembly_sample-R2.fastq.gz" />

            <output name="contigs_outfile" file="abyss-contigs1.fa" />
            <output name="scaffolds" file="abyss-scaffolds1.fa" />
            <output name="indels" file="empty_file.fasta" />
            <output name="stats" file="abyss-stats1.tab" />
        </test>
        <test expect_num_outputs="3">
            <param name="se_reads" ftype="fastq.gz" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
            <param name="k" value="50" />
            <output name="unitigs" file="abyss-unitigs2.fa" />
            <output name="indels" file="empty_file.fasta" />
            <output name="stats" file="abyss-stats2.tab" />
        </test>
        <test expect_num_outputs="4">
            <param name="se_reads" ftype="fasta" value="assembly_sample-R1.fasta,assembly_sample-R2.fasta" />
            <param name="long_seqs" ftype="fasta" value="assembly_sample-R2.fasta" />
            <param name="k" value="50" />
            <output name="unitigs" file="abyss-unitigs3.fa" />
            <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />