comparison metawrapmg_binning.xml @ 2:2a8bc1d26d06 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg commit 26fe7d23c5c3981c9b737109e5db799cc5d23932

1:e3a64a1d2a6e

        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
            ## set memory usage
            if [ -n "\$GALAXY_MEMORY_MB" ] ; then
                GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
            fi ;

            ##################
            ## SET UP FILES ##
            ##################

            ## should always be FASTA
            #set mg_fn = 'metagenome.' + str($metagenome.ext)
            ln -s '$metagenome' $mg_fn
            &&

            ## Only FASTQ. Separate files for each sample. Metawrap checks for
            ## files named _1.fastq and _2.fastq.
            #set input1_fn = 'reads_1.fastq'
            ln -s '$input_1' $input1_fn
            &&

            #set input2_fn = 'reads_2.fastq'
            ln -s '$input_2' $input2_fn
            &&

            #####################
            ## INITIAL BINNING ##
            #####################

            metawrap binning 
            --metabat2 --maxbin2 --concoct 
            -a '$mg_fn'
            -m \${GALAXY_MEMORY_GB:-16}
            -o INITIAL_BINNING
            -t \${GALAXY_SLOTS:-4}
            '$input1_fn'
            '$input2_fn'
            &&

            ## Check which binning programs produced bins            
            bin_dirs=(INITIAL_BINNING/concoct_bins INITIAL_BINNING/maxbin2_bins INITIAL_BINNING/metabat2_bins) &&
            switches=('-A' '-B' '-C') &&

            i=0 &&
            bin_string="" &&

            for dir in "\${bin_dirs[@]}" ; do
                if find "\${dir}" -mindepth 1 -maxdepth 1 | read; then
                    bin_string="\${bin_string} \${switches[\$i]} \${dir}" ;
                    i+=1 ;
                fi
            done &&

            ####################
            ## BIN REFINEMENT ##
            ####################

            ## The checkm database is included in the conda package.
            ## Requires metawrap-mg_1.3.0--hdfd78af_1 or later. See
            ## https://github.com/bioconda/bioconda-recipes/pull/38299.

            metawrap bin_refinement
            -t \${GALAXY_SLOTS:-4}
            -m \${GALAXY_MEMORY_GB:-16}
            -c $binning.c
            -x $binning.x
            -o BIN_REFINEMENT
            ## Only run bin_refinement on bins with contigs
            \${bin_string}
    ]]></command>
    <inputs>
        <param name="metagenome" format="fasta" type="data" label="Metagenome" help="Metagenome co-assembly for binning" />
        <param name="input_1" format="fastqsanger" type="data" label="Read 1" help="Original reads that were used for the assembly: read 1." />
        <param name="input_2" format="fastqsanger" type="data" label="Read 2" help="Original reads that were used for the assembly: read 2." />
        <section name="binning" title="Binning parameters" expanded="false">
            <param argument='-c' type="integer" value="70" min="50" max="100" label="Percent completion" help="Minimum % completion of bins" />
            <param argument='-x' type="integer" value="10" min="0" max="100" label="Percent contamination" help="Maximum % contamination of bins that is acceptable" />
        </section>
    </inputs>
    <outputs>
        <!-- contigs binned into fasta files -->
        <collection name="metawrap_bins" type="list" label="MetaWRAP on ${on_string}: bins">
            <discover_datasets pattern="metawrap_\d+_\d+_bins/(?P&lt;designation&gt;.+)\.fa" format="fasta" directory="BIN_REFINEMENT" recurse="true" match_relative_path="true" visible="false" />
        </collection>
        <!-- summary figures -->
        <collection name="metawrap_figures" type="list" label="MetaWRAP on ${on_string}: summary figures">
            <discover_datasets pattern="__designation_and_ext__" directory="BIN_REFINEMENT/figures" visible="false" />
        </collection>
        <!-- statistics on binning -->
        <collection name="metawrap_stats" type="list" label="MetaWRAP on ${on_string}: stat files">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.stats" format="tabular" directory="BIN_REFINEMENT" visible="false" />
        </collection>
        <!-- which contig went into which bin -->
        <collection name="metawrap_contigs" type="list" label="MetaWRAP on ${on_string}: contig assignments">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.contigs" format="tabular" directory="BIN_REFINEMENT" visible="false" />
        </collection>
    </outputs>
    <tests>
        <!-- 01: basic function -->
        <test>
            <param name="metagenome" value="subset.fasta.gz"/>
            <param name="input_1" value="mapped_reads.r1.fastq.gz"/>
            <param name="input_2" value="mapped_reads.r2.fastq.gz"/>
            <param name="c" value="60"/>
            <param name="x" value="15"/>
            <!-- this is the main output, but it's too large to test -->
            <!-- <output_collection name="metawrap_bins" type="list">
                <element name="bin.1" file="test02.fa" ftype="fasta"/>
            </output_collection> -->
            <output_collection name="metawrap_stats" type="list">
                <element name="metawrap_60_15_bins" file="test02.stats" ftype="tabular"/>
            </output_collection>
            <output_collection name="metawrap_contigs" type="list">
                <element name="metawrap_60_15_bins" file="test02.contigs" ftype="tabular"/>
            </output_collection>
        </test>
    </tests>
        <help><![CDATA[
MetaWRAP
--------

MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that
accomplishes the core tasks of metagenomic analysis. Additionally,

2:2a8bc1d26d06

        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ## set memory usage
        if [ -n "\${GALAXY_MEMORY_MB}" ] ; then
            export GALAXY_MEMORY_GB="\$((GALAXY_MEMORY_MB / 1024))" ;
        fi ;

        ##################
        ## SET UP FILES ##
        ##################

        ## only plain FASTA and FASTQ
        ln -s '$metagenome' metagenome.fasta
        &&
        ## Metawrap checks for files named _1.fastq and _2.fastq.
        ln -s '$input_1' reads_1.fastq
        &&
        ln -s '$input_2' reads_2.fastq
        &&

        #####################
        ## INITIAL BINNING ##
        #####################

        metawrap binning 
        --metabat2 --maxbin2 --concoct 
        -a metagenome.fasta
        -m "\${GALAXY_MEMORY_GB:-16}"
        -o INITIAL_BINNING
        -t "\${GALAXY_SLOTS:-4}"
        reads_1.fastq
        reads_2.fastq
        &&

        ## Check which binning programs produced bins            
        bin_dirs=(INITIAL_BINNING/concoct_bins INITIAL_BINNING/maxbin2_bins INITIAL_BINNING/metabat2_bins) &&
        switches=('-A' '-B' '-C') &&

        i=0 &&
        bin_string="" &&

        for dir in "\${bin_dirs[@]}" ; do
            if [ "\$(find "\$dir" -mindepth 1 -maxdepth 1 -exec echo found \;)" ]; then
                bin_string+=" \${switches[\$i]} \$dir" ;
                ((i++)) ;
            fi
        done &&

        ####################
        ## BIN REFINEMENT ##
        ####################

        ## The checkm database is in the conda package, see
        ## https://github.com/bioconda/bioconda-recipes/pull/38299.

        metawrap bin_refinement
        -t "\${GALAXY_SLOTS:-4}"
        -m "\${GALAXY_MEMORY_GB:-16}"
        '$hidden_quick'
        -c '${binning.c}'
        -x '${binning.x}'
        -o BIN_REFINEMENT
        ## Only run bin_refinement on bins with contigs
        "\${bin_string}"
    ]]></command>
    <inputs>
        <param name="metagenome" format="fasta" type="data" label="Metagenome" help="Metagenome co-assembly for binning"/>
        <param name="input_1" format="fastqsanger" type="data" label="Read 1" help="Original reads that were used for the assembly: read 1."/>
        <param name="input_2" format="fastqsanger" type="data" label="Read 2" help="Original reads that were used for the assembly: read 2."/>
        <section name="binning" title="Binning parameters" expanded="false">
            <param argument="-c" type="integer" value="70" min="50" max="100" label="Percent completion" help="Minimum % completion of bins"/>
            <param argument="-x" type="integer" value="10" min="0" max="100" label="Percent contamination" help="Maximum % contamination of bins that is acceptable"/>
        </section>
        <!-- the pplacer component requires 40 GB per thread. Skip pplacer for
         testing by setting this to "quick" -->
        <param name="hidden_quick" type="hidden" value=""/>
    </inputs>
    <outputs>
        <!-- contigs binned into fasta files -->
        <collection name="metawrap_bins" type="list" label="MetaWRAP on ${on_string}: bins">
            <discover_datasets pattern="metawrap_\d+_\d+_bins/(?P&lt;designation&gt;.+)\.fa" format="fasta" directory="BIN_REFINEMENT" recurse="true" match_relative_path="true"/>
        </collection>
        <!-- summary figures -->
        <collection name="metawrap_figures" type="list" label="MetaWRAP on ${on_string}: summary figures">
            <discover_datasets pattern="__designation_and_ext__" directory="BIN_REFINEMENT/figures"/>
        </collection>
        <!-- statistics on binning -->
        <collection name="metawrap_stats" type="list" label="MetaWRAP on ${on_string}: stat files">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.stats" format="tabular" directory="BIN_REFINEMENT"/>
        </collection>
        <!-- which contig went into which bin -->
        <collection name="metawrap_contigs" type="list" label="MetaWRAP on ${on_string}: contig assignments">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.contigs" format="tabular" directory="BIN_REFINEMENT"/>
        </collection>
    </outputs>
    <tests>
        <!-- 01: basic function -->
        <test>
            <param name="metagenome" value="subset.fasta.gz"/>
            <param name="input_1" value="mapped_reads.r1.fastq.gz"/>
            <param name="input_2" value="mapped_reads.r2.fastq.gz"/>
            <param name="c" value="60"/>
            <param name="x" value="15"/>
            <param name="hidden_quick" value="--quick"/>
            <output_collection name="metawrap_bins" type="list">
                <element name="bin.1" ftype="fasta">
                    <assert_contents>
                        <has_text text="NODE_2_length_"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="metawrap_stats" type="list">
                <element name="metawrap_60_15_bins" file="test02.stats" ftype="tabular"/>
            </output_collection>
            <output_collection name="metawrap_contigs" type="list">
                <element name="metawrap_60_15_bins" file="test02.contigs" ftype="tabular"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
MetaWRAP
--------

MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that
accomplishes the core tasks of metagenomic analysis. Additionally,