annotate trio-mode.xml @ 0:c85aec7804a4 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0

<tool id="meryl_trio_mode" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
    <description>build hap-mers databases for trios</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <xrefs>
        <xref type="bio.tools">meryl</xref>
    </xrefs>
    <expand macro="requirements"/>
    <version_command>meryl --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
    export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ &&
    #if $options_kmer_size.kmer_size == 'estimate'
        #from math import log
        #set size=int(log(int($options_kmer_size.genome_size)*(1-float($options_kmer_size.collision_rate))/float($options_kmer_size.collision_rate))/log(4))
    #elif $options_kmer_size.kmer_size == 'provide'
        #set size=$options_kmer_size.input_kmer_size
    #end if
    #for $i, $read in enumerate($paternal_reads):
        mkdir 'paternal${i}.meryl' &&
        ln -s '$read' ./input_paternal_${i}.${read.ext} &&
        meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_paternal_${i}.${read.ext} output 'paternal${i}.meryl' &&
    #end for
    meryl union-sum paternal*.meryl output pat.meryl &&
    #for $i, $read in enumerate($maternal_reads):
        mkdir 'maternal${i}.meryl' &&
        ln -s '$read' ./input_maternal_${i}.${read.ext} &&
        meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_maternal_${i}.${read.ext} output 'maternal${i}.meryl' &&
    #end for
    meryl union-sum maternal*.meryl output mat.meryl &&
    #for $i, $read in enumerate($child_reads):
        mkdir 'child${i}.meryl' &&
        ln -s '$read' ./input_child_${i}.${read.ext} &&
        meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_child_${i}.${read.ext} output 'child${i}.meryl' &&
    #end for
    meryl union-sum child*.meryl output child.meryl &&
    meryl histogram child.meryl > read-db.hist &&                                          
    tar -czf 'read-db.meryldb' child.meryl &&
    
    ## mat specific kmers
    meryl difference mat.meryl pat.meryl output mat.only.meryl &&
    meryl histogram mat.only.meryl > mat.only.hist &&
    java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.only.hist > mat.only.ploidy &&
    VAR=`sed -n 2p mat.only.ploidy | awk '{print \$NF}'` &&
    meryl greater-than \$VAR output mat.only.filt.meryl mat.only.meryl &&

    ## pat specific kmers
    meryl difference pat.meryl mat.meryl output pat.only.meryl &&
    meryl histogram pat.only.meryl > pat.only.hist &&
    java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.only.hist > pat.only.ploidy &&
    VAR=`sed -n 2p pat.only.ploidy | awk '{print \$NF}'` &&
    meryl greater-than \$VAR output pat.only.filt.meryl pat.only.meryl &&

    ## shared kmers
    meryl intersect output shared.meryl mat.meryl pat.meryl &&

    ## mat hapmers
    meryl intersect output mat.inherited.meryl child.meryl mat.only.filt.meryl &&
    meryl histogram mat.inherited.meryl > mat.inherited.hist &&
    java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.inherited.hist > mat.inherited.ploidy &&
    VAR=`sed -n 2p mat.inherited.ploidy | awk '{print \$NF}'` &&
    meryl greater-than \$VAR output mat.hapmer.meryl mat.inherited.meryl &&
    tar -czf 'mat.meryldb' mat.hapmer.meryl &&

    ## pat hapmers
    meryl intersect output pat.inherited.meryl child.meryl pat.only.filt.meryl &&
    meryl histogram pat.inherited.meryl > pat.inherited.hist &&
    java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy &&
    VAR=`sed -n 2p pat.inherited.ploidy | awk '{print \$NF}'` &&
    meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl &&
    tar -czf 'pat.meryldb' pat.hapmer.meryl &&

    echo 'K-mer size: ${size}'
    ]]></command>
    <inputs>
        <param name="child_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly"/>
        <param name="paternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly"/>
        <param name="maternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly"/>
        <conditional name="options_kmer_size">
            <param name="kmer_size" type="select" label="K-mer size selector">
                <option value="provide">Set a k-mer size</option>
                <option value="estimate">Estimate the best k-mer size</option>
            </param>
            <when value="provide">
                <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G)."/>
            </when>
            <when value="estimate">
                <param name="genome_size" type="integer" min="1000" max="70000000000" value="1000" label="Genome size" help="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided."/>
                <param name="collision_rate" type="float" min="0.0001" max="0.01" value="0.001" label="Tolerable collision rate" help="Tolerable collision rate. By default is 0.001."/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb" label="${tool.name} on ${on_string}: read-db.meryldb"/>
        <data name="read_db_hist" format="tabular" from_work_dir="read-db.hist" label="${tool.name} on ${on_string}: read-db histogram"/>
        <data name="pat_db" format="meryldb" from_work_dir="pat.meryldb" label="${tool.name} on ${on_string}: pat.meryldb"/>
        <data name="pat_db_hist" format="tabular" from_work_dir="pat.inherited.hist" label="${tool.name} on ${on_string}: paternal inherited histogram"/>
        <data name="mat_db" format="meryldb" from_work_dir="mat.meryldb" label="${tool.name} on ${on_string}: mat.meryldb"/>
        <data name="mat_db_hist" format="tabular" from_work_dir="mat.inherited.hist" label="${tool.name} on ${on_string}: maternal inherited histogram"/>
    </outputs>
    <tests>
        <test expect_num_outputs="6">
            <conditional name="options_kmer_size">
                <param name="kmer_size" value="provide"/>
                <param name="input_kmer_size" value="21"/>
            </conditional>
            <param name="maternal_reads" value="maternal.fasta"/>
            <param name="paternal_reads" value="paternal.fasta"/>
            <param name="child_reads" value="child.fasta"/>
            <output name="read_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="3362942" delta="2000"/>
                    <expand macro="meryldb_archive_assumptions"/>
                </assert_contents>
            </output>
            <output name="read_db_hist" file="output_23.read-db.hist"/>
            <output name="pat_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="120610" delta="400"/>
                    <expand macro="meryldb_archive_assumptions"/>
                </assert_contents>
            </output>
            <output name="pat_db_hist" file="output_23.pat.hist"/>
            <output name="mat_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="67883" delta="300"/>
                    <expand macro="meryldb_archive_assumptions"/>
                </assert_contents>
            </output>
            <output name="mat_db_hist" file="output_23.mat.hist"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

Meryl is the k-mer counter. This tool builds hap-mer databases  for trios, in accordance
with `merqury's recommended guidelines. &lt;https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs#3-build-hap-mer-dbs-for-trios&gt;`_

        </help>
    <expand macro="citations"/>
</tool>