comparison meryl.xml @ 2:35ac9de60bec draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"

1:e5b18909f73d

    <expand macro='edam_ontology' />
    <expand macro='requirements' />
    <version_command>meryl --version</version_command>
    <command detect_errors='exit_code'><![CDATA[
        #if $operation_type.command_type == 'count-kmers'
            meryl
            #if $operation_type.options_kmer_size.kmer_size == 'estimate'
                #from math import log
                $operation_type.options_kmer_size.input_kmer_size = int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4))
            #end if
            $operation_type.count_operations
            k=$operation_type.options_kmer_size.input_kmer_size
            $operation_type.input_reads
            output read-db.meryl &&
            echo 'K-mer size: ${$operation_type.options_kmer_size.input_kmer_size}' &&
            tar -zcf read-db.meryldb read-db.meryl
        #elif $operation_type.command_type == 'filter-kmers'
            mkdir  -p ./temp_db/ &&
            tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&
            mv ./temp_db/* tmp.meryl &&

            tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&
            mv ./temp_db/* tmp.meryl &&
            meryl histogram tmp.meryl > read-db.hist
        #elif $operation_type.command_type == 'trio-mode'
            export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ &&
            #for $i, $read in enumerate($paternal_reads):
                mkdir 'paternal{$i}.meryl' &&
                meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'paternal{$i}.meryl' &&
            #end for
            meryl union-sum paternal*.meryl output pat.meryl &&
            #for $i, $read in enumerate($maternal_reads):
                mkdir 'maternal{$i}.meryl' &&
                meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'maternal{$i}.meryl' &&
            #end for
            meryl union-sum maternal*.meryl output mat.meryl &&
            #for $i, $read in enumerate($child_reads):
                mkdir 'child{$i}.meryl' &&
                meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'child{$i}.meryl' &&
            #end for
            meryl union-sum child*.meryl output child.meryl &&
            ## mat specific kmers
            meryl difference mat.meryl pat.meryl output mat.only.meryl &&
            meryl histogram mat.only.meryl > mat.only.hist &&

            
            ## child hapmers
            meryl union-sum output child.inherited.meryl mat.inherited.meryl pat.inherited.meryl shared.inherited.meryl &&
            meryl difference output read.only.meryl child.meryl child.inherited.meryl &&
            tar -czf 'read-db.meryldb' read.only.meryl &&
            echo 'K-mer size: ${$operation_type.options_kmer_size.input_kmer_size}'
        #end if
    ]]>    </command>
    <inputs>
        <conditional name="operation_type">
            <param name="command_type" type="select" label="Operation type selector" help="Select a type of operation">

                    <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="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided." />
                    </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>

                    <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="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided." />
                    </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>

2:35ac9de60bec

    <expand macro='edam_ontology' />
    <expand macro='requirements' />
    <version_command>meryl --version</version_command>
    <command detect_errors='exit_code'><![CDATA[
        #if $operation_type.command_type == 'count-kmers'
            #if $operation_type.options_kmer_size.kmer_size == 'estimate'
                #from math import log
                #set size=int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4))
            #elif $operation_type.options_kmer_size.kmer_size == 'provide'
                #set size=$operation_type.options_kmer_size.input_kmer_size
            #end if
            meryl
            $operation_type.count_operations
            k=$size
            memory=\${GALAXY_MEMORY_GB:-1}
            threads=\${GALAXY_SLOTS:-1}
            $operation_type.input_reads
            output read-db.meryl &&
            echo 'K-mer size: ${size}' &&
            tar -zcf read-db.meryldb read-db.meryl
        #elif $operation_type.command_type == 'filter-kmers'
            mkdir  -p ./temp_db/ &&
            tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&
            mv ./temp_db/* tmp.meryl &&

            tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&
            mv ./temp_db/* tmp.meryl &&
            meryl histogram tmp.meryl > read-db.hist
        #elif $operation_type.command_type == 'trio-mode'
            export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ &&
            #if $operation_type.options_kmer_size.kmer_size == 'estimate'
                #from math import log
                #set size=int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4))
            #elif $operation_type.options_kmer_size.kmer_size == 'provide'
                #set size=$operation_type.options_kmer_size.input_kmer_size
            #end if
            #for $i, $read in enumerate($paternal_reads):
                mkdir 'paternal{$i}.meryl' &&
                meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'paternal{$i}.meryl' &&
            #end for
            meryl union-sum paternal*.meryl output pat.meryl &&
            #for $i, $read in enumerate($maternal_reads):
                mkdir 'maternal{$i}.meryl' &&
                meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'maternal{$i}.meryl' &&
            #end for
            meryl union-sum maternal*.meryl output mat.meryl &&
            #for $i, $read in enumerate($child_reads):
                mkdir 'child{$i}.meryl' &&
                meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'child{$i}.meryl' &&
            #end for
            meryl union-sum child*.meryl output child.meryl &&
            ## mat specific kmers
            meryl difference mat.meryl pat.meryl output mat.only.meryl &&
            meryl histogram mat.only.meryl > mat.only.hist &&

            
            ## child hapmers
            meryl union-sum output child.inherited.meryl mat.inherited.meryl pat.inherited.meryl shared.inherited.meryl &&
            meryl difference output read.only.meryl child.meryl child.inherited.meryl &&
            tar -czf 'read-db.meryldb' read.only.meryl &&
            echo 'K-mer size: ${size}'
        #end if
    ]]>    </command>
    <inputs>
        <conditional name="operation_type">
            <param name="command_type" type="select" label="Operation type selector" help="Select a type of operation">

                    <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>

                    <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>